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Sample records for coli k-12 genome

  1. Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.

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    Brian P Anton

    Full Text Available We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems.

  2. Genes Required for Growth at High Hydrostatic Pressure in Escherichia coli K-12 Identified by Genome-Wide Screening

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    Black, S. Lucas; Dawson, Angela; Ward, F. Bruce; Allen, Rosalind J.

    2013-01-01

    Despite the fact that much of the global microbial biosphere is believed to exist in high pressure environments, the effects of hydrostatic pressure on microbial physiology remain poorly understood. We use a genome-wide screening approach, combined with a novel high-throughput high-pressure cell culture method, to investigate the effects of hydrostatic pressure on microbial physiology in vivo. The Keio collection of single-gene deletion mutants in Escherichia coli K-12 was screened for growth at a range of pressures from 0.1 MPa to 60 MPa. This led to the identification of 6 genes, rodZ, holC, priA, dnaT, dedD and tatC, whose products were required for growth at 30 MPa and a further 3 genes, tolB, rffT and iscS, whose products were required for growth at 40 MPa. Our results support the view that the effects of pressure on cell physiology are pleiotropic, with DNA replication, cell division, the cytoskeleton and cell envelope physiology all being potential failure points for cell physiology during growth at elevated pressure. PMID:24040140

  3. Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

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    Seo, Sang Woo; Gao, Ye; Kim, Donghyuk

    2017-01-01

    A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the osmotic stress response in bacteria. Here, we reveal a genome-scale OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs...... discoveries related to stress responses....

  4. Analysis of RecA-independent recombination events between short direct repeats related to a genomic island and to a plasmid in Escherichia coli K12

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    María F. Azpiroz

    2017-05-01

    Full Text Available RecA-independent recombination events between short direct repeats, leading to deletion of the intervening sequences, were found to occur in two genetic models in the Escherichia coli K12 background. The first model was a small E. coli genomic island which had been shown to be mobile in its strain of origin and, when cloned, also in the E. coli K12 context. However, it did not encode a site-specific recombinase as mobile genomic islands usually do. It was then deduced that the host cells should provide the recombination function. This latter was searched for by means of a PCR approach to detect the island excision in E. coli K12 mutants affected in a number of recombination functions, including the 16 E. coli K12 site-specific recombinases, the RecET system, and multiple proteins that participate in the RecA-dependent pathways of homologous recombination. None of these appeared to be involved in the island excision. The second model, analyzed in a RecA deficient context, was a plasmid construction containing a short direct repeat proceeding from Saccharomyces cerevisiae, which flanked the cat gene. The excision of this gene by recombination of the DNA repeats was confirmed by PCR and through the detection, recovery and characterization of the plasmid deleted form. In sum, we present new evidence on the occurrence of RecA-independent recombination events in E. coli K12. Although the mechanism underlying these processes is still unknown, their existence suggests that RecA-independent recombination may confer mobility to other genetic elements, thus contributing to genome plasticity.

  5. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655

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    Seo, Sang Woo; Kim, Donghyuk; Szubin, Richard

    2015-01-01

    Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. However, their full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OxyR, Sox......R, and SoxS regulons in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 68 genes in 51 transcription units (TUs) belong to these regulons. Among them, 48 genes showed more than 2-fold changes in expression level under single-TF-knockout conditions. This reconstruction expands...

  6. Definition of Additional Flagellar Genes in ESCHERICHIA COLI K12

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    Komeda, Yoshibumi; Kutsukake, Kazuhiro; Iino, Tetsuo

    1980-01-01

    Twenty-nine flagellar genes in Escherichia coli K12 have previously been assigned to three regions of the genome. Flagellar region I is located between pyrC and ptsG, region II between aroD and uvrC, and region III between uvrC and his. In this study, flagellar mutants in Escherichia coli K12 were obtained by selection for resistance to the flagellotropic phage, χ. They were analyzed in complementation tests using P1 phage-mediated transduction. In addition to the fla genes already described,...

  7. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655

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    Sang Woo Seo

    2015-08-01

    Full Text Available Three transcription factors (TFs, OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. However, their full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OxyR, SoxR, and SoxS regulons in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 68 genes in 51 transcription units (TUs belong to these regulons. Among them, 48 genes showed more than 2-fold changes in expression level under single-TF-knockout conditions. This reconstruction expands the genome-wide roles of these factors to include direct activation of genes related to amino acid biosynthesis (methionine and aromatic amino acids, cell wall synthesis (lipid A biosynthesis and peptidoglycan growth, and divalent metal ion transport (Mn2+, Zn2+, and Mg2+. Investigating the co-regulation of these genes with other stress-response TFs reveals that they are independently regulated by stress-specific TFs.

  8. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.

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    Fong, Stephen S; Marciniak, Jennifer Y; Palsson, Bernhard Ø

    2003-11-01

    Genome-scale in silico metabolic networks of Escherichia coli have been reconstructed. By using a constraint-based in silico model of a reconstructed network, the range of phenotypes exhibited by E. coli under different growth conditions can be computed, and optimal growth phenotypes can be predicted. We hypothesized that the end point of adaptive evolution of E. coli could be accurately described a priori by our in silico model since adaptive evolution should lead to an optimal phenotype. Adaptive evolution of E. coli during prolonged exponential growth was performed with M9 minimal medium supplemented with 2 g of alpha-ketoglutarate per liter, 2 g of lactate per liter, or 2 g of pyruvate per liter at both 30 and 37 degrees C, which produced seven distinct strains. The growth rates, substrate uptake rates, oxygen uptake rates, by-product secretion patterns, and growth rates on alternative substrates were measured for each strain as a function of evolutionary time. Three major conclusions were drawn from the experimental results. First, adaptive evolution leads to a phenotype characterized by maximized growth rates that may not correspond to the highest biomass yield. Second, metabolic phenotypes resulting from adaptive evolution can be described and predicted computationally. Third, adaptive evolution on a single substrate leads to changes in growth characteristics on other substrates that could signify parallel or opposing growth objectives. Together, the results show that genome-scale in silico metabolic models can describe the end point of adaptive evolution a priori and can be used to gain insight into the adaptive evolutionary process for E. coli.

  9. The comprehensive updated regulatory network of Escherichia coli K-12

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    Karp Peter D

    2006-01-01

    Full Text Available Abstract Background Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and curating the literature concerning E. coli transcription initiation and operons, providing in both the RegulonDB and EcoCyc databases the largest electronically encoded network available. A paper published recently by Ma et al. (2004 showed several differences in the versions of the network present in these two databases. Discrepancies have been corrected, annotations from this and other groups (Shen-Orr et al., 2002 have been added, making the RegulonDB and EcoCyc databases the largest comprehensive and constantly curated regulatory network of E. coli K-12. Results Several groups have been using these curated data as part of their bioinformatics and systems biology projects, in combination with external data obtained from other sources, thus enlarging the dataset initially obtained from either RegulonDB or EcoCyc of the E. coli K12 regulatory network. We kindly obtained from the groups of Uri Alon and Hong-Wu Ma the interactions they have added to enrich their public versions of the E. coli regulatory network. These were used to search for original references and curate them with the same standards we use regularly, adding in several cases the original references (instead of reviews or missing references, as well as adding the corresponding experimental evidence codes. We also corrected all discrepancies in the two databases available as explained below. Conclusion One hundred and fifty new interactions have been added to our databases as a result of this specific curation effort, in addition to those added as a result of our continuous curation work. RegulonDB gene names are now based on those of EcoCyc to avoid confusion due to gene names and synonyms, and the public releases of RegulonDB and EcoCyc are henceforth synchronized to avoid confusion due to

  10. Development and maturation of Escherichia coli K-12 biofilms

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    Reisner, A.; Haagensen, J.A.J.; Schembri, Mark

    2003-01-01

    The development and maturation of E. coli biofilms in flow-chambers was investigated. We found that the presence of transfer constitutive IncF plasmids induced biofilm development forming structures resembling those reported for Pseudomonas aeruginosa . The development occurred in a step-wise pro......The development and maturation of E. coli biofilms in flow-chambers was investigated. We found that the presence of transfer constitutive IncF plasmids induced biofilm development forming structures resembling those reported for Pseudomonas aeruginosa . The development occurred in a step....... We further provide evidence that flagella, type 1 fimbriae, curli and Ag43 are all dispensable for the observed biofilm maturation. In addition, our results indicate that cell-to-cell signalling mediated by autoinducer 2 (AI-2) is not required for differentiation of E. coli within a biofilm community....... We suggest on the basis of these results that E. coli K-12 biofilm development and maturation is dependent on cell-cell adhesion factors, which may act as inducers of self-assembly processes that result in differently structured biofilms depending on the adhesive properties on the cell surface....

  11. GenoBase: comprehensive resource database of Escherichia coli K-12.

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    Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G; Bochner, Barry R; Conway, Tyrrell; Gribskov, Michael; Kihara, Daisuke; Rudd, Kenneth E; Tohsato, Yukako; Wanner, Barry L; Mori, Hirotada

    2015-01-01

    Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Characterization of pyruvate uptake in Escherichia coli K-12.

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    Jens Kreth

    Full Text Available The monocarboxylate pyruvate is an important metabolite and can serve as sole carbon source for Escherichia coli. Although specific pyruvate transporters have been identified in two bacterial species, pyruvate transport is not well understood in E. coli. In the present study, pyruvate transport was investigated under different growth conditions. The transport of pyruvate shows specific activities depending on the growth substrate used as sole carbon source, suggesting the existence of at least two systems for pyruvate uptake: i one inducible system and probably highly specific for pyruvate and ii one system active under non-induced conditions. Using the toxic pyruvate analog 3-fluoropyruvate, a mutant was isolated unable to grow on and transport pyruvate. Further investigation revealed that a revertant selected for growth on pyruvate regained the inducible pyruvate transport activity. Characterization of pyruvate excretion showed that the pyruvate transport negative mutant accumulated pyruvate in the growth medium suggesting an additional transport system for pyruvate excretion. The here presented data give valuable insight into the pyruvate metabolism and transport of E. coli suggesting the presence of at least two uptake systems and one excretion system to balance the intracellular level of pyruvate.

  13. Characterization of the cyn operon in Escherichia coli K12.

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    Sung, Y C; Fuchs, J A

    1988-10-15

    Escherichia coli can overcome the toxicity of environmental cyanate by hydrolysis of cyanate to ammonia and bicarbonate. This reaction is catalyzed by the enzyme cyanase, encoded by the cynS gene. The nucleotide sequence of cynS has been reported (Sung, Y.-c., Anderson, P. M., and Fuchs, J. A. (1987) J. Bacteriol. 169, 5224-5230). The nucleotide sequence of the complete cyn operon has now been determined. The cyn operon is approximately 2600 base pairs and includes cynT, cynS, and cynX, which encode cyanate permease, cyanase, and a protein of unknown function, respectively. Two cyanate-inducible transcripts of 1500 and 2500 nucleotides, respectively, were detected by Northern blot analysis. S1 nuclease mapping experiments indicated that two different cyn mRNAs have a common 5'-end and two different 3'-ends. One 3'-end was located within the coding region of cynX, whereas the other 3'-end includes the entire DNA sequence of cynX. The longer transcript contained 98 nucleotides complementary to lac mRNA produced by the predominant lac transcription termination sequence. Termination vectors were used to show that both 3'-ends were generated by sequences that caused transcriptional termination in vivo. Expression vectors were used to demonstrate that a protein corresponding to the expected size was synthesized from the DNA fragment containing the open reading frame designated cynX. The predicted amino acid sequence of cynX indicates that it is a very hydrophobic protein. The level of cynX expression was significantly less than that of cynT or cynS expression.

  14. Effects of sound exposure on the growth and intracellular macromolecular synthesis of E. coli k-12

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    Shaobin Gu

    2016-04-01

    Full Text Available Microbes, as one of the primary producers of the biosphere, play an important role in ecosystems. Exploring the mechanism of adaptation and resistance of microbial population to various environmental factors has come into focus in the fields of modern microbial ecology and molecular ecology. However, facing the increasingly serious problem of acoustic pollution, very few efforts have been put forth into studying the relation of single cell organisms and sound field exposure. Herein, we studied the biological effects of sound exposure on the growth of E. coli K-12 with different acoustic parameters. The effects of sound exposure on the intracellular macromolecular synthesis and cellular morphology of E. coli K-12 were also analyzed and discussed. Experimental results indicated that E. coli K-12 exposed to sound waves owned a higher biomass and a faster specific growth rate compared to the control group. Also, the average length of E. coli K-12 cells increased more than 27.26%. The maximum biomass and maximum specific growth rate of the stimulation group by 8000 Hz, 80dB sound wave was about 1.7 times and 2.5 times that of the control group, respectively. Moreover, it was observed that E. coli K-12 can respond rapidly to sound stress at both the transcriptional and posttranscriptional levels by promoting the synthesis of intracellular RNA and total protein. Some potential mechanisms may be involved in the responses of bacterial cells to sound stress.

  15. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle.

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    Denger, Karin; Weiss, Michael; Felux, Ann-Katrin; Schneider, Alexander; Mayer, Christoph; Spiteller, Dieter; Huhn, Thomas; Cook, Alasdair M; Schleheck, David

    2014-03-06

    Sulphoquinovose (SQ, 6-deoxy-6-sulphoglucose) has been known for 50 years as the polar headgroup of the plant sulpholipid in the photosynthetic membranes of all higher plants, mosses, ferns, algae and most photosynthetic bacteria. It is also found in some non-photosynthetic bacteria, and SQ is part of the surface layer of some Archaea. The estimated annual production of SQ is 10,000,000,000 tonnes (10 petagrams), thus it comprises a major portion of the organo-sulphur in nature, where SQ is degraded by bacteria. However, despite evidence for at least three different degradative pathways in bacteria, no enzymic reaction or gene in any pathway has been defined, although a sulphoglycolytic pathway has been proposed. Here we show that Escherichia coli K-12, the most widely studied prokaryotic model organism, performs sulphoglycolysis, in addition to standard glycolysis. SQ is catabolised through four newly discovered reactions that we established using purified, heterologously expressed enzymes: SQ isomerase, 6-deoxy-6-sulphofructose (SF) kinase, 6-deoxy-6-sulphofructose-1-phosphate (SFP) aldolase, and 3-sulpholactaldehyde (SLA) reductase. The enzymes are encoded in a ten-gene cluster, which probably also encodes regulation, transport and degradation of the whole sulpholipid; the gene cluster is present in almost all (>91%) available E. coli genomes, and is widespread in Enterobacteriaceae. The pathway yields dihydroxyacetone phosphate (DHAP), which powers energy conservation and growth of E. coli, and the sulphonate product 2,3-dihydroxypropane-1-sulphonate (DHPS), which is excreted. DHPS is mineralized by other bacteria, thus closing the sulphur cycle within a bacterial community.

  16. Molecular cloning and expression of Treponema pallidum DNA in Escherichia coli K12.

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    J.D.A. van Embden; H.J.M. van de Donk; R.V.W. van Eijk (Ron); H.G. v.d. Heide; J.A. de Jong (Jan); M.F. van Olderen; A.D.M.E. Osterhaus (Albert); L.M. Schouls

    1983-01-01

    textabstractA gene bank of Treponema pallidum DNA in Escherichia coli K-12 was constructed by cloning SauI-cleaved T. pallidum DNA into the cosmid pHC79. Sixteen of 800 clones investigated produced one or more antigens that reacted with antibodies from syphilitic patients. According to the

  17. YbiV from E. coli K12 is a HAD phosphatase

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    Roberts, Anne; Lee, Seok-Yong; McCullagh, Emma; Silversmith, Ruth E.; Wemmer, David E.

    2004-03-16

    The protein YbiV from Escherichia coli K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized ybiV as a HAD phosphatase. The crystal structure of YbiV reveals a two domain protein, one with the characteristic HAD hydrolase fold, the other an inserted a/b fold. In an effort to understand the mechanism we also solved and report the structures of YbiV in complex with beryllofluoride (BeF3-) and aluminum trifluoride (AlF3) which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate ybiV may be a sugar phosphatase, which is supported by biochemical assays which measured the release of free phosphate on a number of sugar-like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate.

  18. Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12.

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    Shimada, Tomohiro; Momiyama, Eri; Yamanaka, Yuki; Watanabe, Hiroki; Yamamoto, Kaneyoshi; Ishihama, Akira

    2017-12-01

    The genome of Escherichia coli K-12 contains ten cryptic phages, altogether constituting about 3.6% of the genome in sequence. Among more than 200 predicted genes in these cryptic phages, 14 putative transcription factor (TF) genes exist, but their regulatory functions remain unidentified. As an initial attempt to make a breakthrough for understanding the regulatory roles of cryptic phage-encoded TFs, we tried to identify the regulatory function of CP4-6 cryptic prophage-encoded YagI with unknown function. After SELEX screening, YagI was found to bind mainly at a single site within the spacer of bidirectional transcription units, yagA (encoding another uncharacterized TF) and yagEF (encoding 2-keto-3-deoxy gluconate aldolase, and dehydratase, respectively) within this prophage region. YagEF enzymes are involved in the catabolism of xylose downstream from xylonate. We then designated YagI as XynR (regulator of xylonate catabolism), one of the rare single-target TFs. In agreement with this predicted regulatory function, the activity of XynR was suggested to be controlled by xylonate. Even though low-affinity binding sites of XynR were identified in the E. coli K-12 genome, they all were inside open reading frames, implying that the regulation network of XynR is still fixed within the CR4-6 prophage without significant influence over the host E. coli K-12. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Characterization of the specific pyruvate transport system in Escherichia coli K-12.

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    Lang, V J; Leystra-Lantz, C; Cook, R A

    1987-01-01

    A mutant of Escherichia coli K-12 lacking pyruvate dehydrogenase and phosphoenolpyruvate synthase was used to study the transport of pyruvate by whole cells. Uptake of pyruvate was maximal in mid-log phase cells, with a Michaelis constant for transport of 20 microM. Pretreatment of the cells with respiratory chain poisons or uncouplers, except for arsenate, inhibited transport up to 95%. Lactate and alanine were competitive inhibitors, but at nonphysiological concentrations. The synthetic ana...

  20. Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression

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    Beloin, C.; Valle, J.; Latour-Lambert, P.

    2004-01-01

    The formation of biofilm results in a major lifestyle switch that is thought to affect the expression of multiple genes and operons. We used DNA arrays to study the global effect of biofilm formation on gene expression in mature Escherichia coli K-12 biofilm. We show that, when biofilm is compared...... that 20 of these genes are required for the formation of mature biofilm. This group includes 11 genes of previously unknown function. These results constitute a comprehensive analysis of the global transcriptional response triggered in mature E. coli biofilms and provide insights into its physiological...

  1. Characterization of the specific pyruvate transport system in Escherichia coli K-12.

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    Lang, V J; Leystra-Lantz, C; Cook, R A

    1987-01-01

    A mutant of Escherichia coli K-12 lacking pyruvate dehydrogenase and phosphoenolpyruvate synthase was used to study the transport of pyruvate by whole cells. Uptake of pyruvate was maximal in mid-log phase cells, with a Michaelis constant for transport of 20 microM. Pretreatment of the cells with respiratory chain poisons or uncouplers, except for arsenate, inhibited transport up to 95%. Lactate and alanine were competitive inhibitors, but at nonphysiological concentrations. The synthetic analogs 3-bromopyruvate and pyruvic acid methyl ester inhibited competitively. The uptake of pyruvate was also characterized in membrane vesicles from wild-type E. coli K-12. Transport required an artificial electron donor system, phenazine methosulfate and sodium ascorbate. Pyruvate was concentrated in vesicles 7- to 10-fold over the external concentration, with a Michaelis constant of 15 microM. Energy poisons, except arsenate, inhibited the transport of pyruvate. Synthetic analogs such as 3-bromopyruvate were competitive inhibitors of transport. Lactate initially appeared to be a competitive inhibitor of pyruvate transport in vesicles, but this was a result of oxidation of lactate to pyruvate. The results indicate that uptake of pyruvate in E. coli is via a specific active transport system.

  2. Biochemical and genetic characterization of a carbamyl phosphate synthetase mutant of Escherichia coli K12.

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    Bolivar, F; Galván, M; Martuscelli, J

    1976-05-01

    An unusual Escherichia coli K12 mutant for carbamyl phosphate synthetase is described. The mutation was generated by bacteriophage MUI insertion and left a 5% residual activity of the enzyme using either ammonia or glutamine as donors. The mutation is recessive to the wild-type allele and maps at or near the pyrA gene, but the mutant requires only arginine and not uracil for growth. By a second block in the pyrB gene it was possible to shift the accumulated carbamyl phosphate to arginine biosynthesis. The Km values and the levels of ornithine activation and inhibition by UMP were normal in the mutant enzyme.

  3. The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

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    Keseler, Ingrid M; Mackie, Amanda; Santos-Zavaleta, Alberto; Billington, Richard; Bonavides-Martínez, César; Caspi, Ron; Fulcher, Carol; Gama-Castro, Socorro; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Muñiz-Rascado, Luis; Ong, Quang; Paley, Suzanne; Peralta-Gil, Martin; Subhraveti, Pallavi; Velázquez-Ramírez, David A; Weaver, Daniel; Collado-Vides, Julio; Paulsen, Ian; Karp, Peter D

    2017-01-04

    EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Associations of Escherichia coli K-12 OmpF trimers with rough and smooth lipopolysaccharides

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    Diedrich, D.L.; Stein, M.A.; Schnaitman, C.A. (Louisiana State Univ. Medical Center, New Orleans (USA))

    1990-09-01

    The associations of both rough and smooth lipopolysaccharides (LPS) with the OmpF porin of Escherichia coli K-12 were examined in galE strains deleted for ompC. Transformation with pSS37 and growth with galactose conferred the ability to assemble a Shigella dysenteriae O antigen onto the core oligosaccharide of E. coli K-12 LPS. The association of LPS with OmpF trimers was assessed by staining, autoradiography of LPS specifically labeled with (1-14C)galactose, and Western immunoblotting with a monoclonal antibody specific for OmpF trimers. These techniques revealed that the migration distances and multiple banding patterns of OmpF porin trimers in sodium dodecyl sulfate-polyacrylamide gels were dictated by the chemotype of associated LPS. Expression of smooth LPS caused almost all of the trimeric OmpF to run in gels with a slower mobility than trimers from rough strains. The LPS associated with trimers from a smooth strain differed from the bulk-phase LPS by consisting almost exclusively of molecules with O antigen.

  5. Leaner and meaner genomes in Escherichia coli

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    Ussery, David

    2006-01-01

    A 'better' Escherichia coli K-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. Comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions....

  6. Escherichia coli K-12 pathogenicity in the pea aphid, Acyrthosiphon pisum, reveals reduced antibacterial defense in aphids.

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    Altincicek, Boran; Ter Braak, Bas; Laughton, Alice M; Udekwu, Klas I; Gerardo, Nicole M

    2011-10-01

    To better understand the molecular basis underlying aphid immune tolerance to beneficial bacteria and immune defense to pathogenic bacteria, we characterized how the pea aphid Acyrthosiphon pisum responds to Escherichia coli K-12 infections. E. coli bacteria, usually cleared in the hemolymph of other insect species, were capable of growing exponentially and killing aphids within a few days. Red fluorescence protein expressing E. coli K-12 laboratory strain multiplied in the aphid hemolymph as well as in the digestive tract, resulting in death of infected aphids. Selected gene deletion mutants of the E. coli K-12 predicted to have reduced virulence during systemic infections showed no difference in either replication or killing rate when compared to the wild type E. coli strain. Of note, however, the XL1-Blue E. coli K-12 strain exhibited a significant lag phase before multiplying and killing aphids. This bacterial strain has recently been shown to be more sensitive to oxidative stress than other E. coli K-12 strains, revealing a potential role for reactive oxygen species-mediated defenses in the otherwise reduced aphid immune system. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Antigen 43 and type 1 fimbriae determine colony morphology of Escherichia coli K-12

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    Hasman, Henrik; Schembri, Mark; Klemm, Per

    2000-01-01

    Colony morphology has been used as an important identification and characterization criterion in bacteriology for many decades. However, the molecular mechanisms underlying the appearance of different colony types have been given little attention. The synthesis of O antigen is defunct in Escheric......Colony morphology has been used as an important identification and characterization criterion in bacteriology for many decades. However, the molecular mechanisms underlying the appearance of different colony types have been given little attention. The synthesis of O antigen is defunct...... in Escherichia coli K-12, and colonies should accordingly only appear to be rough. However, previous reports have noted the presence of different interchangeable colony morphology types. In this study we have addressed the influence of two phase-variable surface structures, antigen 43 and type 1 fimbriae...

  8. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions

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    Edwards Jeremy S

    2000-07-01

    Full Text Available Abstract Background Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silico representations of integrated metabolic functions can be constructed and analyzed using flux balance analysis (FBA. FBA is particularly well-suited to study metabolic networks based on genomic, biochemical, and strain specific information. Results Herein, we have utilized FBA to interpret and analyze the metabolic capabilities of Escherichia coli. We have computationally mapped the metabolic capabilities of E. coli using FBA and examined the optimal utilization of the E. coli metabolic pathways as a function of environmental variables. We have used an in silico analysis to identify seven gene products of central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, electron transport system essential for aerobic growth of E. coli on glucose minimal media, and 15 gene products essential for anaerobic growth on glucose minimal media. The in silico tpi-, zwf, and pta- mutant strains were examined in more detail by mapping the capabilities of these in silico isogenic strains. Conclusions We found that computational models of E. coli metabolism based on physicochemical constraints can be used to interpret mutant behavior. These in silica results lead to a further understanding of the complex genotype-phenotype relation. Supplementary information: http://gcrg.ucsd.edu/supplementary_data/DeletionAnalysis/main.htm

  9. Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism.

    Science.gov (United States)

    He, Amanda; Penix, Stephanie R; Basting, Preston J; Griffith, Jessie M; Creamer, Kaitlin E; Camperchioli, Dominic; Clark, Michelle W; Gonzales, Alexandra S; Chávez Erazo, Jorge Sebastian; George, Nadja S; Bhagwat, Arvind A; Slonczewski, Joan L

    2017-06-15

    Acid-adapted strains of Escherichia coli K-12 W3110 were obtained by serial culture in medium buffered at pH 4.6 (M. M. Harden, A. He, K. Creamer, M. W. Clark, I. Hamdallah, K. A. Martinez, R. L. Kresslein, S. P. Bush, and J. L. Slonczewski, Appl Environ Microbiol 81:1932-1941, 2015, https://doi.org/10.1128/AEM.03494-14). Revised genomic analysis of these strains revealed insertion sequence (IS)-driven insertions and deletions that knocked out regulators CadC (acid induction of lysine decarboxylase), GadX (acid induction of glutamate decarboxylase), and FNR (anaerobic regulator). Each acid-evolved strain showed loss of one or more amino acid decarboxylase systems, which normally help neutralize external acid (pH 5 to 6) and increase survival in extreme acid (pH 2). Strains from populations B11, H9, and F11 had an IS 5 insertion or IS-mediated deletion in cadC , while population B11 had a point mutation affecting the arginine activator adiY The cadC and adiY mutants failed to neutralize acid in the presence of exogenous lysine or arginine. In strain B11-1, reversion of an rpoC (RNA polymerase) mutation partly restored arginine-dependent neutralization. All eight strains showed deletion or downregulation of the Gad acid fitness island. Strains with the Gad deletion lost the ability to produce GABA (gamma-aminobutyric acid) and failed to survive extreme acid. Transcriptome sequencing (RNA-seq) of strain B11-1 showed upregulated genes for catabolism of diverse substrates but downregulated acid stress genes (the biofilm regulator ariR , yhiM , and Gad). Other strains showed downregulation of H 2 consumption mediated by hydrogenases ( hya and hyb ) which release acid. Strains F9-2 and F9-3 had a deletion of fnr and showed downregulation of FNR-dependent genes ( dmsABC , frdABCD , hybABO , nikABCDE , and nrfAC ). Overall, strains that had evolved in buffered acid showed loss or downregulation of systems that neutralize unbuffered acid and showed altered regulation of

  10. Gene envY of Escherichia coli K-12 affects thermoregulation of major porin expression.

    Science.gov (United States)

    Lundrigan, M D; Earhart, C F

    1984-01-01

    The temperature-dependent expression of OmpF and OmpC, the major channel-forming proteins of the Escherichia coli K-12 outer membrane, was studied. In wild-type cells, decreasing growth temperatures resulted in increased amounts of OmpF protein and correspondingly decreased quantities of OmpC protein. Bacteria deleted for the 13-min chromosomal region did not exhibit this temperature-dependent fluctuation in porin proteins. Plasmid pML22, which consists of pBR322 containing a 0.5-megadalton E. coli chromosomal DNA insert, complemented the thermoregulatory defect. The regulatory gene was named envY. In minicells, pML22 directed the synthesis of an envelope polypeptide (EnvY) having an apparent molecular weight of 25,000. The EnvY protein was synthesized in minicells in greater amounts at 27 degrees C than at 37 degrees C, and a reducing agent was necessary in the solubilization buffer for its subsequent detection on polyacrylamide gels. The results describe the initial characterization of a regulatory system which, along with proteins of the ompB operon, the cyclic AMP system, and the tolC gene product, is involved in a complex network affecting major porin expression. Images PMID:6317653

  11. Precise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r

    DEFF Research Database (Denmark)

    Michelsen, Ole; de Mattos, M.J.T.; Jensen, Peter Ruhdal

    2003-01-01

    The C and D cell cycle periods of seven Escherichia coli K-12 strains and three E, coli B/r strains were determined by computer simulation of DNA histograms obtained by flow cytometry of batch cultures grown at several different generation times. To obtain longer generation times two of the K-12...... generation times. In glucose-limited chemostats good correlation was found between D periods and generation times, whereas batch cultures exhibited carbon-source-dependent variations. Chemostat cultures showed cell cycle variations very similar to those obtained in batch cultures. These flow cytometric...

  12. Mechanism for nitrogen isotope fractionation during ammonium assimilation by Escherichia coli K12

    Science.gov (United States)

    Vo, Jason; Inwood, William; Hayes, John M.; Kustu, Sydney

    2013-01-01

    Organisms that use ammonium as the sole nitrogen source discriminate between [15N] and [14N] ammonium. This selectivity leaves an isotopic signature in their biomass that depends on the external concentration of ammonium. To dissect how differences in discrimination arise molecularly, we examined a wild-type (WT) strain of Escherichia coli K12 and mutant strains with lesions affecting ammonium-assimilatory proteins. We used isotope ratio mass spectrometry (MS) to assess the nitrogen isotopic composition of cell material when the strains were grown in batch culture at either high or low external concentrations of NH3 (achieved by controlling total NH4Cl and pH of the medium). At high NH3 (≥0.89 µM), discrimination against the heavy isotope by the WT strain (−19.2‰) can be accounted for by the equilibrium isotope effect for dissociation of NH4+ to NH3 + H+. NH3 equilibrates across the cytoplasmic membrane, and glutamine synthetase does not manifest an isotope effect in vivo. At low NH3 (≤0.18 µM), discrimination reflects an isotope effect for the NH4+ channel AmtB (−14.1‰). By making E. coli dependent on the low-affinity ammonium-assimilatory pathway, we determined that biosynthetic glutamate dehydrogenase has an inverse isotope effect in vivo (+8.8‰). Likewise, by making unmediated diffusion of NH3 across the cytoplasmic membrane rate-limiting for cell growth in a mutant strain lacking AmtB, we could deduce an in vivo isotope effect for transport of NH3 across the membrane (−10.9‰). The paper presents the raw data from which our conclusions were drawn and discusses the assumptions underlying them. PMID:23650377

  13. Mechanism for nitrogen isotope fractionation during ammonium assimilation by Escherichia coli K12.

    Science.gov (United States)

    Vo, Jason; Inwood, William; Hayes, John M; Kustu, Sydney

    2013-05-21

    Organisms that use ammonium as the sole nitrogen source discriminate between [(15)N] and [(14)N] ammonium. This selectivity leaves an isotopic signature in their biomass that depends on the external concentration of ammonium. To dissect how differences in discrimination arise molecularly, we examined a wild-type (WT) strain of Escherichia coli K12 and mutant strains with lesions affecting ammonium-assimilatory proteins. We used isotope ratio mass spectrometry (MS) to assess the nitrogen isotopic composition of cell material when the strains were grown in batch culture at either high or low external concentrations of NH3 (achieved by controlling total NH4Cl and pH of the medium). At high NH3 (≥ 0.89 µM), discrimination against the heavy isotope by the WT strain (-19.2‰) can be accounted for by the equilibrium isotope effect for dissociation of NH4(+) to NH3 + H(+). NH3 equilibrates across the cytoplasmic membrane, and glutamine synthetase does not manifest an isotope effect in vivo. At low NH3 (≤ 0.18 µM), discrimination reflects an isotope effect for the NH4(+) channel AmtB (-14.1‰). By making E. coli dependent on the low-affinity ammonium-assimilatory pathway, we determined that biosynthetic glutamate dehydrogenase has an inverse isotope effect in vivo (+8.8‰). Likewise, by making unmediated diffusion of NH3 across the cytoplasmic membrane rate-limiting for cell growth in a mutant strain lacking AmtB, we could deduce an in vivo isotope effect for transport of NH3 across the membrane (-10.9‰). The paper presents the raw data from which our conclusions were drawn and discusses the assumptions underlying them.

  14. PEF based hurdle strategy to control Pichia fermentans, Listeria innocua and Escherichia coli k12 in orange juice.

    Science.gov (United States)

    McNamee, C; Noci, F; Cronin, D A; Lyng, J G; Morgan, D J; Scannell, A G M

    2010-03-31

    The combination of pulsed electric fields (PEF) and bacteriocins in a hurdle approach has been reported to enhance microbial inactivation. This study investigates the preservation of orange juice using PEF in combination with nisin (2.5 ppm), natamycin (10 ppm), benzoic acid (BA; 100 ppm), or lactic acid, (LA; 500 ppm). Pichia fermentans, a spoilage yeast frequently isolated from orange juice, Escherichia coli k12 or Listeria innocua were inoculated into sterile orange juice (OJ) with, and without, added preservatives. The antimicrobial activity over time was evaluated relative to an untreated control. The effect of PEF treatment (40 kV/cm, 100 micros; max temperature 56 degrees C) was assessed on its own, and in combination with each antimicrobial. The acidic environment of OJ inactivated E. coli k12 (1.5log reduction) and L. innocua (0.7log reduction) slightly but had no effect on P. fermentans. PEF caused a significant decrease (PPEF inactivated L. innocua and E. coli k12 in a synergistic manner resulting in a total reduction to 5.6 and 7.9log respectively. A similar synergy was shown between LA and PEF in the inactivation of L. innocua and P. fermentans (6.1 and 7.8log reduction), but not E. coli k12. The BA-PEF combination caused an additive inactivation of P. fermentans, whereas the natamycin-PEF combination against P. fermentans was not significantly different to the effect caused by PEF alone. This study shows that combining PEF with the chosen preservatives, at levels lower than those in current use, can provide greater than 5log reductions of E. coli k12, L. innocua and P. fermentans in OJ. These PEF-bio-preservative combination hurdles could provide the beverage industry with effective non-thermal alternatives to prevent microbial spoilage, and improve the safety of fruit juice. Copyright 2009 Elsevier B.V. All rights reserved.

  15. GENE TRANSFER BY F′ STRAINS OF ESCHERICHIA COLI K-12 II.

    Science.gov (United States)

    Pittard, James; Adelberg, Edward A.

    1963-01-01

    Pittard, James (Yale University, New Haven, Conn.) and Edward A. Adelberg. Gene transfer by F′ strains of Escherichia coli K-12. II. Interaction between F-merogenote and chromosome during transfer. J. Bacteriol. 85:1402–1408. 1963.—When F′ strains harboring the F-merogenate F14 are mated with female recipients, the transfer of the F-merogenote begins, in the majority of cases, before chromosome transfer. The markers on F14 are transferred in the sequence met-1, arg-1, ilva-16, and sex-factor, met-1 being transferred first and sex-factor being transferred last, 9 min after met-1. In the class of zygotes that have received both the F-merogenote marker met-1 and the chromosomal marker xyl or mal, the gradient of recombination frequencies for the F-merogenote markers arg-1 and ilva-16 is much steeper than in the corresponding zygotes that have not received chromosomal markers. In F′ strains which exhibit an increased frequency of transfer of chromosome markers, this gradient of recombination frequencies for merogenote markers is much steeper. An analysis of experiments involving an F′ strain with a much shorter F-merogenote, F16, and of a triparental mating in which F-merogenote and chromosome were transferred from different donor cells reveals that the effect of chromosome transfer on the recovery of distal F-merogenote markers in the zygotes is not due to any form of postzygotic elimination. It is suggested that, when F′ strains which are transferring F-merogenote begin to transfer chromosome, the latter event causes breakage of the F-merogenote. A second consequence of this interaction is a delay of 8 to 10 min in the first appearance of chromosomal markers in the zygotes. PMID:14047236

  16. Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.

    Science.gov (United States)

    Gama-Castro, Socorro; Rinaldi, Fabio; López-Fuentes, Alejandra; Balderas-Martínez, Yalbi Itzel; Clematide, Simon; Ellendorff, Tilia Renate; Santos-Zavaleta, Alberto; Marques-Madeira, Hernani; Collado-Vides, Julio

    2014-01-01

    Given the current explosion of data within original publications generated in the field of genomics, a recognized bottleneck is the transfer of such knowledge into comprehensive databases. We have for years organized knowledge on transcriptional regulation reported in the original literature of Escherichia coli K-12 into RegulonDB (http://regulondb.ccg.unam.mx), our database that is currently supported by >5000 papers. Here, we report a first step towards the automatic biocuration of growth conditions in this corpus. Using the OntoGene text-mining system (http://www.ontogene.org), we extracted and manually validated regulatory interactions and growth conditions in a new approach based on filters that enable the curator to select informative sentences from preprocessed full papers. Based on a set of 48 papers dealing with oxidative stress by OxyR, we were able to retrieve 100% of the OxyR regulatory interactions present in RegulonDB, including the transcription factors and their effect on target genes. Our strategy was designed to extract, as we did, their growth conditions. This result provides a proof of concept for a more direct and efficient curation process, and enables us to define the strategy of the subsequent steps to be implemented for a semi-automatic curation of original literature dealing with regulation of gene expression in bacteria. This project will enhance the efficiency and quality of the curation of knowledge present in the literature of gene regulation, and contribute to a significant increase in the encoding of the regulatory network of E. coli. RegulonDB Database URL: http://regulondb.ccg.unam.mx OntoGene URL: http://www.ontogene.org. © The Author(s) 2014. Published by Oxford University Press.

  17. Attachment behaviour of Escherichia coli K12 and Salmonella Typhimurium P6on food contact surfaces for food transportation

    DEFF Research Database (Denmark)

    Abban, Stephen; Jakobsen, Mogens; Jespersen, Lene

    2012-01-01

    . Typhimurium P6 respectively. Correlation with roughness average was poor; r = -0.425 and -0.413 respectively for E. coli K12 and S. Typhimurium P6. Presence of residue caused significant reduction (p bacteria attached to all materials, but made attached bacteria significantly more...... difficult to detach by either of two rinsing systems from all three surfaces. Explanation for these observations could be made in part from scanning electron micrographs which showed significantly more bacteria sitting on patches of residue when it was introduced to the surfaces, compared to the bare...... material sections of the same surfaces. We report these observations for the first time for aluminium and the FRP material and in part for stainless steel. The S. Typhimurium P6 strain also had significantly higher level of attachment than the E. coli K12 strain. Our findings show that food residue...

  18. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

    DEFF Research Database (Denmark)

    Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.

    2017-01-01

    Adaptive laboratory evolution (ALE) is a widely-used method for improving the fitness of microorganisms in selected environmental conditions. It has been applied previously to Escherichia coli K-12 MG1655 during aerobic exponential growth on glucose minimal media, a frequently used model organism...... principal components. The distance between measured and flux balance analysis predicted fluxes was also investigated. It suggested a relatively wide range of similar stoichiometric optima, which opens new questions about the path-dependency of adaptive evolution....

  19. Attachment behaviour of Escherichia coli K12 and Salmonella Typhimurium P6 on food contact surfaces for food transportation.

    Science.gov (United States)

    Abban, Stephen; Jakobsen, Mogens; Jespersen, Lene

    2012-09-01

    The role of cargo container lining materials aluminium, a fibre reinforced plastic (FRP) and stainless steel in bacterial cross contamination during transport was assessed. For this, attachment and detachment of Escherichia coli K12 and Salmonella Typhimurium P6 on the three surfaces in the absence or presence of residues were evaluated. Observations were correlated with water contact angles of the materials (hydrophobicity) and roughness profile (R(a)). Attachment of the organisms was negatively correlated to the hydrophobicity of the three materials with r = -0.869 and -0.861 for E. coli K12 and S. Typhimurium P6 respectively. Correlation with roughness average was poor; r = -0.425 and -0.413 respectively for E. coli K12 and S. Typhimurium P6. Presence of residue caused significant reduction (p food residue and soils affect the extent and amount of bacteria attaching to abiotic surfaces by altering the surface contact properties for the bacteria. Physicochemical properties like hydrophobicity appear to be a better basis for material selection for hygienic design of containers, than the traditional use of R(a). Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Graphene-Based FET Detector for E. coli K12 Real-Time Monitoring and Its Theoretical Analysis

    Directory of Open Access Journals (Sweden)

    Jieyi Zhu

    2016-01-01

    Full Text Available This paper presents a theoretical analysis for a graphene-based FET real-time detector of the target bacteria E. coli K12. The motivation for this study is to design a sensor device for detection of bacteria in food and water in order to guarantee food safety. Graphene is chosen as our material for sensor design, which has outstanding electrical, physical, and optical performance. In our sensor structure, graphene-based solution gate field effect transistor (FET is the device model; fabrication and functionalization protocol are presented together in this paper. What is more, a real-time signal display system is the accompanied equipment for our designed biosensor device. In this system, the sensor bias current signal Ids would change obviously when the target bacteria are attached to the sensor surface. And the bias current Ids increases when the E. coli concentration increases. In the latter part, a theoretical interpretation of the sensor signal is to explain the bias current Ids increasing after the E. coli K12 attachment.

  1. Biogenic synthesis and characterization of gold nanoparticles by Escherichia coli K12 and its heterogeneous catalysis in degradation of 4-nitrophenol

    National Research Council Canada - National Science Library

    Srivastava, Sarvesh Kumar; Yamada, Ryosuke; Ogino, Chiaki; Kondo, Akihiko

    2013-01-01

    Room-temperature extracellular biosynthesis of gold nanoparticles (Au NPs) was achieved using Escherichia coli K12 cells without the addition of growth media, pH adjustments or inclusion of electron donors/stabilizing agents...

  2. Functional analysis of the large periplasmic loop of the Escherichia coli K-12 WaaL O-antigen ligase.

    Science.gov (United States)

    Pérez, José M; McGarry, Megan A; Marolda, Cristina L; Valvano, Miguel A

    2008-12-01

    WaaL is a membrane enzyme implicated in ligating undecaprenyl-diphosphate (Und-PP)-linked O antigen to lipid A-core oligosaccharide. We determined the periplasmic location of a large (EL5) and small (EL4) adjacent loops in the Escherichia coli K-12 WaaL. Structural models of the EL5 from the K-12, R1 and R4 E. coli ligases were generated by molecular dynamics. Despite the poor amino acid sequence conservation among these proteins, the models afforded similar folds consisting of two pairs of almost perpendicular alpha-helices. One alpha-helix in each pair contributes a histidine and an arginine facing each other, which are highly conserved in WaaL homologues. Mutations in either residue rendered WaaL non-functional, since mutant proteins were unable to restore O antigen surface expression. Replacements of residues located away from the putative catalytic centre and non-conserved residues within the centre itself did not affect ligation. Furthermore, replacing a highly conserved arginine in EL4 with various amino acids inactivates WaaL function, but functionality reappears when the positive charge is restored by a replacement with lysine. These results lead us to propose that the conserved amino acids in the two adjacent periplasmic loops could interact with Und-PP, which is the common component in all WaaL substrates.

  3. Identification and characterization of a cyanate permease in Escherichia coli K-12.

    Science.gov (United States)

    Sung, Y C; Fuchs, J A

    1989-09-01

    Escherichia coli contains an inducible enzyme, cyanase, that catalyzes the decomposition of cyanate into ammonia and bicarbonate. The gene encoding cyanase, cynS, was cloned and found to be on a DNA fragment that contained the lac operon. Characterization of a plasmid encoding cyanase indicated that a 26-kilodalton (kDa) protein of unknown function was also induced by cyanate (Y-C. Sung, D. Parsell, P.M. Anderson, and J.A. Fuchs, J. Bacteriol. 169:2639-2642, 1987). The gene encoding the 26-kDa protein was located between cynS and its promoter, indicating the existence of a cyn operon. The 26-kDa protein was identified as a cyanate permease that transports exogenous cyanate by active transport. E. coli was shown to contain a cyanate transport system that is energy dependent and saturable by cyanate.

  4. The Putrescine Importer PuuP of Escherichia coli K-12

    Science.gov (United States)

    Kurihara, Shin; Tsuboi, Yuichi; Oda, Shinpei; Kim, Hyeon Guk; Kumagai, Hidehiko; Suzuki, Hideyuki

    2009-01-01

    The Puu pathway is a putrescine utilization pathway involving gamma-glutamyl intermediates. The genes encoding the enzymes of the Puu pathway form a gene cluster, the puu gene cluster, and puuP is one of the genes in this cluster. In Escherichia coli, three putrescine importers, PotFGHI, PotABCD, and PotE, were discovered in the 1990s and have been studied; however, PuuP had not been discovered previously. This paper shows that PuuP is a novel putrescine importer whose kinetic parameters are equivalent to those of the polyamine importers discovered previously. A puuP+ strain absorbed up to 5 mM putrescine from the medium, but a ΔpuuP strain did not. E. coli strain MA261 has been used in previous studies of polyamine transporters, but PuuP had not been identified previously. It was revealed that the puuP gene of MA261 was inactivated by a point mutation. When E. coli was grown on minimal medium supplemented with putrescine as the sole carbon or nitrogen source, only PuuP among the polyamine importers was required. puuP was expressed strongly when putrescine was added to the medium or when the puuR gene, which encodes a putative repressor, was deleted. When E. coli was grown in M9-tryptone medium, PuuP was expressed mainly in the exponential growth phase, and PotFGHI was expressed independently of the growth phase. PMID:19181795

  5. The Escherichia coli K-12 gntP gene allows E. coli F-18 to occupy a distinct nutritional niche in the streptomycin-treated mouse large intestine

    DEFF Research Database (Denmark)

    Sweeney, N.J.; Klemm, Per; McCormick, Beth A.

    1996-01-01

    Escherichia coli F-18 is a human fecal isolate that makes type 1 fimbriae, encoded by the fim gene cluster, and is an excellent colonizer of the streptomycin-treated mouse intestine. E. coli F-18 fimA::tet, lacking type 1 fimbriae, was constructed by bacteriophage P1 transduction of the fim region...... of the E. coli K-12 strain ORN151, containing the tetracycline resistance gene from Tn10 inserted in the fimA gene, into E. coli F-18. E. coli F-18 fimA::tet was found to occupy a distinct niche in the streptomycin-treated mouse intestine when fed in small numbers to mice, along with large numbers of E....... coli K-12 gene responsible for this effect is not fim::tet but gntP, which maps immidiately downstream of the fim gene cluster, are presented. gntP encodes a high-affinity gluconate permease, suggesting that the distinct niche in the mouse large intestine is defined by the presence of gluconate...

  6. Identification, mapping, and cloning of the gene encoding cyanase in Escherichia coli K-12.

    Science.gov (United States)

    Sung, Y C; Parsell, D; Anderson, P M; Fuchs, J A

    1987-06-01

    The gene in Escherichia coli for cyanase, designated cynS, was localized to a BglII restriction site approximately 1.7 kilobases from the lacA end of the lac operon. The gene was cloned into the pUC13 vector. Maxicell analysis of plasmid-encoded proteins confirmed that the BglII site is in the region encoding the structural gene for cyanase. Cyanase-deficient strains had increased sensitivity to cyanate and were not able to use cyanate as a nitrogen source.

  7. Identification, mapping, and cloning of the gene encoding cyanase in Escherichia coli K-12.

    OpenAIRE

    Sung, Y C; Parsell, D; Anderson, P M; Fuchs, J A

    1987-01-01

    The gene in Escherichia coli for cyanase, designated cynS, was localized to a BglII restriction site approximately 1.7 kilobases from the lacA end of the lac operon. The gene was cloned into the pUC13 vector. Maxicell analysis of plasmid-encoded proteins confirmed that the BglII site is in the region encoding the structural gene for cyanase. Cyanase-deficient strains had increased sensitivity to cyanate and were not able to use cyanate as a nitrogen source.

  8. Identification and characterization of a cyanate permease in Escherichia coli K-12.

    OpenAIRE

    Sung, Y C; Fuchs, J A

    1989-01-01

    Escherichia coli contains an inducible enzyme, cyanase, that catalyzes the decomposition of cyanate into ammonia and bicarbonate. The gene encoding cyanase, cynS, was cloned and found to be on a DNA fragment that contained the lac operon. Characterization of a plasmid encoding cyanase indicated that a 26-kilodalton (kDa) protein of unknown function was also induced by cyanate (Y-C. Sung, D. Parsell, P.M. Anderson, and J.A. Fuchs, J. Bacteriol. 169:2639-2642, 1987). The gene encoding the 26-kD...

  9. Metabolic Engineering of Escherichia coli K12 for Homofermentative Production of L-Lactate from Xylose.

    Science.gov (United States)

    Jiang, Ting; Zhang, Chen; He, Qin; Zheng, Zhaojuan; Ouyang, Jia

    2018-02-01

    The efficient utilization of xylose is regarded as a technical barrier to the commercial production of bulk chemicals from biomass. Due to the desirable mechanical properties of polylactic acid (PLA) depending on the isomeric composition of lactate, biotechnological production of lactate with high optical pure has been increasingly focused in recent years. The main objective of this work was to construct an engineered Escherichia coli for the optically pure L-lactate production from xylose. Six chromosomal deletions (pflB, ldhA, ackA, pta, frdA, adhE) and a chromosomal integration of L-lactate dehydrogenase-encoding gene (ldhL) from Bacillus coagulans was involved in construction of E. coli KSJ316. The recombinant strain could produce L-lactate from xylose resulting in a yield of 0.91 g/g xylose. The chemical purity of L-lactate was 95.52%, and the optical purity was greater than 99%. Moreover, three strategies, including overexpression of L-lactate dehydrogenase, intensification of xylose catabolism, and addition of additives to medium, were designed to enhance the production. The results showed that they could increase the concentration of L-lactate by 32.90, 20.13, and 233.88% relative to the control, respectively. This was the first report that adding formate not only could increase the xylose utilization but also led to the fewer by-product levels.

  10. Investigation on the anaerobic propionate degradation by Escherichia coli K12.

    Science.gov (United States)

    Simonte, Francesca M; Dötsch, Andreas; Galego, Lisete; Arraiano, Cecilia; Gescher, Johannes

    2017-01-01

    Propionate is an abundant carboxylic acid in nature. Microorganisms metabolize propionate aerobically via the 2-methylcitrate pathway. This pathway depends on a series of three reactions in the citric acid cycle that leads to the conversion of succinate to oxaloacetate. Interestingly, the γ-proteobacterium Escherichia coli can use propionate as a carbon and electron source under oxic but not under anoxic conditions. RT-PCR and transcriptomic analysis revealed a posttranscriptional regulation of the prpBCDE-gene cluster encoding the necessary enzymes for propionate metabolism. The polycistronic mRNA seems to be hydrolyzed in the 3'-5' direction under anoxic conditions. This regulatory strategy is highly constructive because the last gene of the operon encodes the first enzyme of the propionate metabolism. Further analysis revealed that RNase R is involved in the hydrolysis of the prp transcripts. Consequently, an rnr-deletion strain could metabolize propionate under anoxic conditions. To the best of our knowledge, this is the first study describing the influence of RNase R on the anaerobic metabolism of E. coli. © 2016 John Wiley & Sons Ltd.

  11. A comparative analysis of industrial Escherichia coli K-12 and B strains in high-glucose batch cultivations on process-, transcriptome- and proteome level.

    Directory of Open Access Journals (Sweden)

    Karoline Marisch

    Full Text Available Escherichia coli K-12 and B strains are among the most frequently used bacterial hosts for production of recombinant proteins on an industrial scale. To improve existing processes and to accelerate bioprocess development, we performed a detailed host analysis. We investigated the different behaviors of the E. coli production strains BL21, RV308, and HMS174 in response to high-glucose concentrations. Tightly controlled cultivations were conducted under defined environmental conditions for the in-depth analysis of physiological behavior. In addition to acquisition of standard process parameters, we also used DNA microarray analysis and differential gel electrophoresis (Ettan(TM DIGE. Batch cultivations showed different yields of the distinct strains for cell dry mass and growth rate, which were highest for BL21. In addition, production of acetate, triggered by excess glucose supply, was much higher for the K-12 strains compared to the B strain. Analysis of transcriptome data showed significant alteration in 347 of 3882 genes common among all three hosts. These differentially expressed genes included, for example, those involved in transport, iron acquisition, and motility. The investigation of proteome patterns additionally revealed a high number of differentially expressed proteins among the investigated hosts. The subsequently selected 38 spots included proteins involved in transport and motility. The results of this comprehensive analysis delivered a full genomic picture of the three investigated strains. Differentially expressed groups for targeted host modification were identified like glucose transport or iron acquisition, enabling potential optimization of strains to improve yield and process quality. Dissimilar growth profiles of the strains confirm different genotypes. Furthermore, distinct transcriptome patterns support differential regulation at the genome level. The identified proteins showed high agreement with the transcriptome data

  12. Development of an Escherichia coli K12-specific quantitative polymerase chain reaction assay and DNA isolation suited to biofilms associated with iron drinking water pipe corrosion products

    Science.gov (United States)

    Escherichia coli is one of the most commonly used fecal indicator organisms for drinking water and groundwater systems. In order to understand various biogeochemical and biophysical factors affecting its interactions with biofilms, E. coli K12 was chosen as a model organism. A Ta...

  13. Immunoglobulin-Mediated Agglutination of and Biofilm Formation by Escherichia coli K-12 Require the Type 1 Pilus Fiber

    Science.gov (United States)

    Orndorff, Paul E.; Devapali, Aditya; Palestrant, Sarah; Wyse, Aaron; Everett, Mary Lou; Bollinger, R. Randal; Parker, William

    2004-01-01

    The binding of human secretory immunoglobulin A (SIgA), the primary immunoglobulin in the gut, to Escherichia coli is thought to be dependent on type 1 pili. Type 1 pili are filamentous bacterial surface attachment organelles comprised principally of a single protein, the product of the fimA gene. A minor component of the pilus fiber (the product of the fimH gene, termed the adhesin) mediates attachment to a variety of host cell molecules in a mannose inhibitable interaction that has been extensively described. We found that the aggregation of E. coli K-12 by human secretory IgA (SIgA) was dependent on the presence of the pilus fiber, even in the absence of the mannose specific adhesin or in the presence of 25 mM α-CH3Man. The presence of pilus without adhesin also facilitated SIgA-mediated biofilm formation on polystyrene, although biofilm formation was stronger in the presence of the adhesin. IgM also mediated aggregation and biofilm formation in a manner dependent on pili with or without adhesin. These findings indicate that the pilus fiber, even in the absence of the adhesin, may play a role in biologically important processes. Under conditions in which E. coli was agglutinated by SIgA, the binding of SIgA to E. coli was not increased by the presence of the pili, with or without adhesin. This observation suggests that the pili, with or without adhesin, affect factors such as cell surface rigidity or electrostatic repulsion, which can affect agglutination but which do not necessarily determine the level of bound immunoglobulin. PMID:15039312

  14. Development of an Escherichia coli K12-specific quantitative polymerase chain reaction assay and DNA isolation suited to biofilms associated with iron drinking water pipe corrosion products.

    Science.gov (United States)

    Lu, Jingrang; Gerke, Tammie L; Buse, Helen Y; Ashbolt, Nicholas J

    2014-12-01

    A quantitative polymerase chain reaction assay (115 bp amplicon) specific to Escherichia coli K12 with an ABI(TM) internal control was developed based on sequence data encoding the rfb gene cluster. Assay specificity was evaluated using three E. coli K12 strains (ATCC W3110, MG1655 & DH1), 24 non-K12 E. coli and 23 bacterial genera. The biofilm detection limit was 10(3) colony-forming units (CFU) E. coli K12 mL(-1), but required a modified protocol, which included a bio-blocker Pseudomonas aeruginosa with ethylenediaminetetraacetic acid buffered to pH 5 prior to cell lysis/DNA extraction. The novel protocol yielded the same sensitivity for drinking water biofilms associated with Fe3O4 (magnetite)-coated SiO2 (quartz) grains and biofilm-surface iron corrosion products from a drinking water distribution system. The novel DNA extraction protocol and specific E. coli K12 assay are sensitive and robust enough for detection and quantification within iron drinking water pipe biofilms, and are particularly well suited for studying enteric bacterial interactions within biofilms.

  15. The UDP-glucose dehydrogenase of Escherichia coli K-12 displays substrate inhibition by NAD that is relieved by nucleotide triphosphates.

    Science.gov (United States)

    Mainprize, Iain L; Bean, Jordan D; Bouwman, Catrien; Kimber, Matthew S; Whitfield, Chris

    2013-08-09

    UDP-glucose dehydrogenase (Ugd) generates UDP-glucuronic acid, an important precursor for the production of many hexuronic acid-containing bacterial surface glycostructures. In Escherichia coli K-12, Ugd is important for biosynthesis of the environmentally regulated exopolysaccharide known as colanic acid, whereas in other E. coli isolates, the same enzyme is required for production of the constitutive group 1 capsular polysaccharides, which act as virulence determinants. Recent studies have implicated tyrosine phosphorylation in the activation of Ugd from E. coli K-12, although it is not known if this is a feature shared by bacterial Ugd proteins. The activities of Ugd from E. coli K-12 and from the group 1 capsule prototype (serotype K30) were compared. Surprisingly, for both enzymes, site-directed Tyr → Phe mutants affecting the previously proposed phosphorylation site retained similar kinetic properties to the wild-type protein. Purified Ugd from E. coli K-12 had significant levels of NAD substrate inhibition, which could be alleviated by the addition of ATP and several other nucleotide triphosphates. Mutations in a previously identified UDP-glucuronic acid allosteric binding site decreased the binding affinity of the nucleotide triphosphate. Ugd from E. coli serotype K30 was not inhibited by NAD, but its activity still increased in the presence of ATP.

  16. Transformation of Escherichia coli K-12 with a high-copy plasmid encoding the green fluorescent protein reduces growth: implications for predictive microbiology.

    Science.gov (United States)

    Oscar, T P; Dulal, K; Boucaud, D

    2006-02-01

    The green fluorescent protein (GFP) of the jellyfish Aequorea victoria has been widely used as a biomarker and has potential for use in developing predictive models for growth of pathogens on naturally contaminated food. However, constitutive production of GFP can reduce growth of transformed strains. Consequently, a high-copy plasmid with gfp under the control of a tetracycline-inducible promoter (pTGP) was constructed. The plasmid was first introduced into a tetracycline-resistant strain of Escherichia coli K-12 to propagate it for subsequent transformation of tetracycline-resistant strains of Salmonella. In contrast to transformed E. coli K-12, which only fluoresced in response to tetracycline, transformed Salmonella fluoresced maximally without tetracycline induction of gfp. Although pTGP did not function as intended in Salmonella, growth of parent and GFP E. coli K-12 was compared to test the hypothesis that induction of GFP production reduced growth. Although GFP production was not induced during growth on sterile chicken in the absence of tetracycline, maximum specific growth rate (mumax) of GFP E. coli K-12 was reduced 40 to 50% (P E. coli K-12 was compared in sterile broth at 40 degrees C, mumax and maximum population density of the GFP strain were reduced (P transformation reduced growth of E. coli K-12 independent of gfp induction. Thus, use of a low-copy plasmid or insertion of gfp into the chromosome may be required to construct valid strains for development of predictive models for growth of pathogens on naturally contaminated food.

  17. An Investigative Study on the Effect of Silver Nanoparticles on E.Coli K12 in Various Sodium Chloride Concentrations

    Science.gov (United States)

    Levard, C.; Mitra, S.; Badireddy, A.; Jew, A. D.; Brown, G. E.

    2011-12-01

    Engineered nanomaterials have had an increasing presence in consumer products. Consequently, their release in wastewater systems is believed to pose a viable threat to the environment. NPs are used for drug delivery devices, imaging agents, and consumer products like sunscreens, paints, and cosmetics. Among the major types of manufactured nanoparticles, silver nanoparticles (Ag-NPs) are currently the most widely used in the nanotechnology industry. These particles have unique antibacterial, antiviral, and antifungal properties and as a result, there is a growing concern about the environmental impact of released Ag nanoparticles, particularly their unintended impact on organisms and ecosystems. Even though the toxicity of Ag-NPs has been extensively studied, the environmental transformations that the Ag-NPs may experience once released in the environment have not been considered. These transformations can readily impact their properties and therefore their behavior in terms of reactivity and toxicity. For example, it is known that silver strongly react with Chloride (Cl), which is ubiquitous in natural waters. At a low Cl/Ag ratio, Cl may precipitate on the surface and partly inhibit dissolution. On the contrary, for a high Cl/Ag ratio, chloride may enhance dissolution and therefore toxicity since soluble Ag species are a main source of toxicity. In this context, the focus of this study is on understanding the toxicity of coated Ag-NPs at various concentrations (1ppb-100ppm) on E.Coli (K12) in deionized water and various sodium chloride concentrations that mimic natural conditions (.5, .1 and .01 M NaCl). Ag+ ions (100 ppm-1ppb) were also tested in these salt concentrations as a control. Samples were inoculated in bacteria and incubated for 24 hours. Based on this test, we inferred that increasing concentrations of Ag+ ions/ AgNps played a role in the inhibition of growth of E.Coli K12. A live-dead staining test has shown the correlation between inhibition of

  18. Bidirectional frequency-dependent effect of extremely low-frequency electromagnetic field on E. coli K-12.

    Science.gov (United States)

    Martirosyan, Varsik; Baghdasaryan, Naira; Ayrapetyan, Sinerik

    2013-09-01

    In the present work, the frequency-dependent effects of extremely low-frequency electromagnetic field (ELF EMF) on Escherichia coli K-12 growth have been studied. The frequency-dependent effects of ELF EMF have shown that it can either stimulate or inhibit the growth of microbes. However, the mechanism by which the ELF EMF affects the bacterial cells is not clear yet. It was suggested that the aqua medium can serve as a target through which the biological effect of ELF EMF on microbes may be realized. To check this hypothesis, the frequency-dependent effects (2, 4, 6, 8, 10 Hz, B = 0.4 mT, 30 min) of ELF EMF on the bacterial growth were studied in both cases where the microbes were in the culture media during the exposure and where culture media was preliminarily exposed to the ELF EMF before the addition of bacteria. For investigating the cell proliferation, the radioactive [(3)H]-thymidine assay was carried out. It has been shown that EMF at 4 Hz exposure has pronounced stimulation while at 8 Hz it has inhibited cell proliferation.

  19. Cryopreservation of Escherichia coli K12TG1: protection from the damaging effects of supercooling by freezing.

    Science.gov (United States)

    Simonin, H; Bergaoui, I M; Perrier-Cornet, J M; Gervais, P

    2015-04-01

    Injuries in living cells caused by water freezing during a freeze-thaw process have been extensively reported. In particular, intracellular water freezing has long been incriminated in cell death caused by a high cooling rate, but this supposition could not always be demonstrated. This work aims to discriminate the role of water freezing, dehydration and cold-induced injuries in cellular damage occuring during cryopreservation. For this purpose, Escherichia coli K12TG1 suspensions were maintained in a supercooled or frozen state at -20°C for times ranging from 10 min to 5 h. The supercooled state was maintained for a long period at -20°C by applying a non-injurious isostatic pressure (Pfreezing, the survival rate remained high throughout the experiment, and the cell membranes suffered little damage. Moreover, cells subjected to 5h of osmotic treatments at -20°C, conditions that mimic cryoconcentration upon freezing, and subsequently diluted and thawed suffered little damage. Dehydration due to cryoconcentration upon freezing protects the cells against the deleterious effects of supercooling, especially in the plasma membranes. The decrease in membrane leakage upon dehydration at low temperatures could be linked to differences in the gel state of the membrane revealed by a higher Laurdan general polarization (GP) value. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.

    Science.gov (United States)

    Salgado, Heladia; Gama-Castro, Socorro; Martínez-Antonio, Agustino; Díaz-Peredo, Edgar; Sánchez-Solano, Fabiola; Peralta-Gil, Martín; Garcia-Alonso, Delfino; Jiménez-Jacinto, Verónica; Santos-Zavaleta, Alberto; Bonavides-Martínez, César; Collado-Vides, Julio

    2004-01-01

    RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of transcriptional regulation in Escherichia coli K-12. This includes mechanistic information about operon organization and their decomposition into transcription units (TUs), promoters and their sigma type, binding sites of specific transcriptional regulators (TRs), their organization into 'regulatory phrases', active and inactive conformations of TRs, as well as terminators and ribosome binding sites. The database is complemented with clearly marked computational predictions of TUs, promoters and binding sites of TRs. The current version has been expanded to include information beyond specific mechanisms aimed at gathering different growth conditions and the associated induced and/or repressed genes. RegulonDB is now linked with Swiss-Prot, with microarray databases, and with a suite of programs to analyze and visualize microarray experiments. We provide a summary of the biological knowledge contained in RegulonDB and describe the major changes in the design of the database. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/.

  1. GENE TRANSFER BY F' STRAINS OF ESCHERICHIA COLI K-12. II. INTERACTION BETWEEN F-MEROGENOTE AND CHROMOSOME DURING TRANSFER.

    Science.gov (United States)

    PITTARD, J; ADELBERG, E A

    1963-06-01

    Pittard, James (Yale University, New Haven, Conn.) and Edward A. Adelberg. Gene transfer by F' strains of Escherichia coli K-12. II. Interaction between F-merogenote and chromosome during transfer. J. Bacteriol. 85:1402-1408. 1963.-When F' strains harboring the F-merogenate F(14) are mated with female recipients, the transfer of the F-merogenote begins, in the majority of cases, before chromosome transfer. The markers on F(14) are transferred in the sequence met-1, arg-1, ilva-16, and sex-factor, met-1 being transferred first and sex-factor being transferred last, 9 min after met-1. In the class of zygotes that have received both the F-merogenote marker met-1 and the chromosomal marker xyl or mal, the gradient of recombination frequencies for the F-merogenote markers arg-1 and ilva-16 is much steeper than in the corresponding zygotes that have not received chromosomal markers. In F' strains which exhibit an increased frequency of transfer of chromosome markers, this gradient of recombination frequencies for merogenote markers is much steeper. An analysis of experiments involving an F' strain with a much shorter F-merogenote, F(16), and of a triparental mating in which F-merogenote and chromosome were transferred from different donor cells reveals that the effect of chromosome transfer on the recovery of distal F-merogenote markers in the zygotes is not due to any form of postzygotic elimination. It is suggested that, when F' strains which are transferring F-merogenote begin to transfer chromosome, the latter event causes breakage of the F-merogenote. A second consequence of this interaction is a delay of 8 to 10 min in the first appearance of chromosomal markers in the zygotes.

  2. Characterization of high-level expression and sequencing of the Escherichia coli K-12 cynS gene encoding cyanase.

    Science.gov (United States)

    Sung, Y C; Anderson, P M; Fuchs, J A

    1987-11-01

    Restriction fragments containing the gene encoding cyanase, cynS, without its transcriptional regulatory sequences were placed downstream of lac and tac promoters in various pUC derivatives to maximize production of cyanase. Plasmid pSJ105, which contains the cynS gene and an upstream open reading frame, gave the highest expression of cyanase. Approximately 50% of the total soluble protein in stationary-phase cultures of a lac-deleted strain containing plasmid pSJ105 was cyanase. The inserted DNA fragment of pSJ105 was transferred into pUC18 derivatives that contain a hybrid tac promoter, instead of the lac promoter, and a strong terminator to generate pSJ124. Stationary-phase cultures of JM101 containing plasmid pSJ124 overexpressed a similar level of cyanase. In JM101(pSJ124), maximum production of cyanase could be obtained either by induction with isopropyl-beta-D-thiogalactopyranoside (IPTG) for 3 h or by growth without IPTG into late stationary phase. The latter conditions resulted in a 10- to 20-fold increase in plasmid content and presumably titration of the lac repressor. The nucleotide sequence of the cloned cynS gene from Escherichia coli K-12 was determined. The predicted amino acid sequence differed from the known amino acid sequence of cyanase isolated from a B strain by four residues. However, overexpressed cyanase was purified to homogeneity, and a comparison of the enzymes from the two sources indicated that they did not differ with respect to physical and kinetic properties. The cynS gene was located next to the lac operon, and the direction of cynS transcription was opposite that of lac.

  3. Membrane damage and viability loss of Escherichia coli K-12 and Salmonella enteritidis in liquid egg by thermal death time disk treatment.

    Science.gov (United States)

    Ukuku, Dike O; Jin, Tony; Zhang, Howard

    2008-10-01

    Bacterial injury, including leakage of intracellular substance and viability loss, of Escherichia coli K-12 (ATCC 23716) and Salmonella Enteritidis (ATCC 13076) inoculated in liquid egg white and liquid whole egg was determined by thermal death time disk. E. coli K-12 and Salmonella Enteritidis were inoculated in liquid egg white and liquid whole egg to a final count of 7.8 log CFU/ml and were thermally treated with thermal death time disks at room temperature (23"C), 54, 56, 58, and 60 degrees C from 0 to 240 s. Sublethal injury, leakage of intracellular substances, and viability loss of E. coli K-12 and Salmonella Enteritidis was investigated by plating 0.1 ml on selective trypticase soy agar containing 3% NaCl, 5% NaCl, sorbitol MacConky agar, and xylose lysine sodium tetradecylsulfate and nonselective trypticase soy agar. No significant (P > 0.05) differences on percent injury or viability loss for E. coli K-12 and Salmonella populations were determined in all samples treated at 23 degrees C. Sublethal injury occurred in E. coli and Salmonella populations at 54 degrees C or above for 120 s. Viability losses for both bacteria averaged 5 log at 54 degrees C or above for 180 s, and the surviving populations were below detection (membrane damage, leakage, and accumulation of intracellular ATP from 2 to 2.5 log fg/ml and UV-absorbing substances of 0.1 to 0.39 in the treated samples. These results indicate similar thermal injury/damage on both E. coli and Salmonella membranes as determined by the amount of inactivation, viability loss, and leakage of intracellular substances of bacteria.

  4. Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer.

    Science.gov (United States)

    Kingston, Anthony W; Ponkratz, Christine; Raleigh, Elisabeth A

    2017-04-01

    Bacteria use a variety of DNA-mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real-world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. In the study described here, we investigated the uncharacterized family of YhgA-like transposase_31 (Pfam PF04754) proteins. Our primary focus was the genetic and biochemical properties of the five Escherichia coli K-12 members of this family, which we designate RpnA to RpnE, where Rpn represents r ecombination- p romoting n uclease. We employed a conjugal system developed by our lab that demanded RecA-independent recombination following transfer of chromosomal DNA. Overexpression of RpnA (YhgA), RpnB (YfcI), RpnC (YadD), and RpnD (YjiP) increased RecA-independent recombination, reduced cell viability, and induced the expression of reporter of DNA damage. For the exemplar of the family, RpnA, mutational changes in proposed catalytic residues reduced or abolished all three phenotypes in concert. In vitro , RpnA displayed magnesium-dependent, calcium-stimulated DNA endonuclease activity with little, if any, sequence specificity and a preference for double-strand cleavage. We propose that Rpn/YhgA-like family nucleases can participate in gene acquisition processes. IMPORTANCE Bacteria adapt to new environments by obtaining new genes from other bacteria. Here, we characterize a set of genes that can promote the acquisition process by a novel mechanism. Genome comparisons had suggested the horizontal spread of the genes for the YhgA-like family of proteins through bacteria. Although annotated as transposase_31, no member of the family has previously been characterized experimentally. We show that four Escherichia coli K-12 paralogs contribute to a novel RecA-independent recombination mechanism in vivo For RpnA, we demonstrate in vitro action as a magnesium-dependent, calcium-stimulated nonspecific DNA endonuclease. The

  5. Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3

    Directory of Open Access Journals (Sweden)

    Charlier Daniel

    2011-04-01

    fluxes. In addition, a comparison of the genome sequences of the two strains showed that BL21 possesses two mutations in the promoter region of iclR and rare codons are present in arcA implying a lower tRNA acceptance. Both phenomena presumably result in a reduced ArcA and IclR synthesis in BL21, which contributes to the similar physiology as observed in E. coli K12 ΔarcAΔiclR. Conclusions The deletion of arcA results in a decrease of repression on transcription of TCA cycle genes under glucose abundant conditions, without significantly affecting the glyoxylate pathway activity. IclR clearly represses transcription of glyoxylate pathway genes under glucose abundance, a condition in which Crp activation is absent. Under glucose limitation, Crp is responsible for the high glyoxylate flux, but IclR still represses transcription. Finally, in E. coli BL21 (DE3, ArcA and IclR are poorly expressed, explaining the similar fluxes observed compared to the ΔarcAΔiclR strain.

  6. Regulation of 3-Deoxy-d-arabino-Heptulosonic 7-Phosphate Acid Synthetase Activity in Relation to the Synthesis of the Aromatic Vitamins in Escherichia coli K-12

    Science.gov (United States)

    Wallace, B. J.; Pittard, J.

    1969-01-01

    Both in vivo and in vitro experiments on wild-type Escherichia coli K-12 and mutant strains possessing only single 3-deoxy-d-arabino-heptulosonic 7-phosphate acid (DAHP) synthetase isoenzymes indicated that, under conditions when all three isoenzymes are fully repressed, sufficient chorismate is still formed for the synthesis of aromatic vitamins. Under repressed conditions both DAHP synthetase (phe) and (trp), but not DAHP synthetase (tyr), were shown to contribute to vitamin production. PMID:4905534

  7. A novel role for RecA under non-stress: promotion of swarming motility in Escherichia coli K-12

    Directory of Open Access Journals (Sweden)

    Blázquez Jesús

    2007-03-01

    Full Text Available Abstract Background Bacterial motility is a crucial factor in the colonization of natural environments. Escherichia coli has two flagella-driven motility types: swimming and swarming. Swimming motility consists of individual cell movement in liquid medium or soft semisolid agar, whereas swarming is a coordinated cellular behaviour leading to a collective movement on semisolid surfaces. It is known that swimming motility can be influenced by several types of environmental stress. In nature, environmentally induced DNA damage (e.g. UV irradiation is one of the most common types of stress. One of the key proteins involved in the response to DNA damage is RecA, a multifunctional protein required for maintaining genome integrity and the generation of genetic variation. Results The ability of E. coli cells to develop swarming migration on semisolid surfaces was suppressed in the absence of RecA. However, swimming motility was not affected. The swarming defect of a ΔrecA strain was fully complemented by a plasmid-borne recA gene. Although the ΔrecA cells grown on semisolidsurfaces exhibited flagellar production, they also presented impaired individual movement as well as a fully inactive collective swarming migration. Both the comparative analysis of gene expression profiles in wild-type and ΔrecA cells grown on a semisolid surface and the motility of lexA1 [Ind-] mutant cells demonstrated that the RecA effect on swarming does not require induction of the SOS response. By using a RecA-GFP fusion protein we were able to segregate the effect of RecA on swarming from its other functions. This protein fusion failed to regulate the induction of the SOS response, the recombinational DNA repair of UV-treated cells and the genetic recombination, however, it was efficient in rescuing the swarming motility defect of the ΔrecA mutant. The RecA-GFP protein retains a residual ssDNA-dependent ATPase activity but does not perform DNA strand exchange. Conclusion

  8. Nucleotide sequence, mutational analysis, transcriptional start site, and product analysis of nov, the gene which affects Escherichia coli K-12 resistance to the gyrase inhibitor novobiocin.

    Science.gov (United States)

    Ivanisevic, R; Milić, M; Ajdić, D; Rakonjac, J; Savić, D J

    1995-04-01

    In a previous study, we demonstrated the existence of a gene locus, nov, which affects resistance of Escherichia coli K-12 to the gyrase inhibitor novobiocin and, to a lesser degree, coumermycin (J. Rakonjac, M. Milic, D. Ajdic, D. Santos, R. Ivanisevic, and D. J. Savic, Mol. Microbiol. 6:1547-1553, 1992). In the present study, sequencing of the nov gene locus revealed one open reading frame that encodes a protein of 54,574 Da, a value. found to be in correspondence with the size of the Nov protein identified in an in vitro translation system. We also located the 5' end of the nov transcript 8 bp downstream from a classical sigma70 promoter. Transcription of the gene is in the counterclockwise direction on the E. coli chromosome. Transposon mutagenesis of nov followed by complementation analyses and replacement of chromosomal alleles with mutated nov confirmed our previous assumption that the nov gene exists in two allelic forms and that the Novr gene is an active allele while the Novs gene is an inactive form. After comparing nucleotide sequences flanking the nov gene with existing data, we conclude that the gene order in this region of the E. coli K-12 map is att phi 80-open reading frame of unknown function-kch (potassium channel protein)-nov-opp. Finally, the possible identity of the nov gene with cls, the gene that codes for cardiolipin synthase, is also discussed.

  9. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

    DEFF Research Database (Denmark)

    McCloskey, Douglas; Palsson, Bernhard; Feist, Adam

    2013-01-01

    The genome-scale model (GEM) of metabolism in the bacterium Escherichia coli K-12 has been in development for over a decade and is now in wide use. GEM-enabled studies of E. coli have been primarily focused on six applications: (1) metabolic engineering, (2) model-driven discovery, (3) prediction...

  10. The nucleotide sequence of aroG, the gene for 3-deoxy-D-arabinoheptulosonate-7-phosphate synthetase (phe) in Escherichia coli K 12

    OpenAIRE

    Davies, W.David; Davidson, Barrie E.

    1982-01-01

    We have determined the nucleotide sequence of aroG, the gene coding for 3-deoxy-D-arabinoheptulosonate-7-phosphate synthetase(phe), one of three isoenzymes that catalyse the first step of the biosynthesis of aromatic amino acids and vitamins in Escherichia coli K12. The DNA sequence agrees with previously published data on the N-terminal sequence, amino acid composition, and subunit molecular weight of 3-deoxy-D-arabinoheptulosonate-7-phosphate synthetase(phe). There is significant identity i...

  11. Mechanism for regulation of the putrescine utilization pathway by the transcription factor PuuR in Escherichia coli K-12.

    Science.gov (United States)

    Nemoto, Naoki; Kurihara, Shin; Kitahara, Yuzuru; Asada, Kei; Kato, Kenji; Suzuki, Hideyuki

    2012-07-01

    In Escherichia coli, putrescine is metabolized to succinate for use as a carbon and nitrogen source by the putrescine utilization pathway (Puu pathway). One gene in the puu gene cluster encodes a transcription factor, PuuR, which has a helix-turn-helix DNA-binding motif. DNA microarray analysis of an E. coli puuR mutant, in which three amino acid residues in the helix-turn-helix DNA binding motif of PuuR were mutated to alanine to eliminate DNA binding of PuuR, suggested that PuuR is a negative regulator of puu genes. Results of gel shift and DNase I footprint analyses suggested that PuuR binds to the promoter regions of puuA and puuD. The binding of wild-type PuuR to a DNA probe containing PuuR recognition sites was diminished with increasing putrescine concentrations in vitro. These results suggest that PuuR regulates the intracellular putrescine concentration by the transcriptional regulation of genes in the Puu pathway, including puuR itself. The puu gene cluster is found in E. coli and closely related enterobacteria, but this gene cluster is uncommon in other bacterial groups. E. coli and related enterobacteria may have gained the Puu pathway as an adaptation for survival in the mammalian intestine, an environment in which polyamines exist at relatively high concentrations.

  12. Biogenic synthesis and characterization of gold nanoparticles by Escherichia coli K12 and its heterogeneous catalysis in degradation of 4-nitrophenol

    Science.gov (United States)

    Srivastava, Sarvesh Kumar; Yamada, Ryosuke; Ogino, Chiaki; Kondo, Akihiko

    2013-02-01

    Room-temperature extracellular biosynthesis of gold nanoparticles (Au NPs) was achieved using Escherichia coli K12 cells without the addition of growth media, pH adjustments or inclusion of electron donors/stabilizing agents. The resulting nanoparticles were analysed by ultraviolet-visible (UV-vis) spectrophotometry, atomic force microscopy, transmission electron microscopy and X-ray diffraction. Highly dispersed gold nanoplates were achieved in the order of around 50 nm. Further, the underlying mechanism was found to be controlled by certain extracellular membrane-bound proteins, which was confirmed by Fourier transformation-infrared spectroscopy and sodium dodecyl sulfate polyacrylamide gel electrophoresis. We observed that certain membrane-bound peptides are responsible for reduction and subsequent stabilization of Au NPs (confirmed by zeta potential analysis). Upon de-activation of these proteins, no nanoparticle formation was observed. Also, we prepared a novel biocatalyst with Au NPs attached to the membrane-bound fraction of E. coli K12 cells serving as an efficient heterogeneous catalyst in complete reduction of 4-nitrophenol in the presence of NaBH4 which was studied with UV-vis spectroscopy. This is the first report on bacterial membrane-Au NP nanobiocomposite serving as an efficient heterogeneous catalyst in complete reduction of nitroaromatic pollutant in water.

  13. Formation of a lambda (Tn10) tyrR+ specialized transducing bacteriophage from Escherichia coli K-12.

    Science.gov (United States)

    Cobbett, C S; Pittard, J

    1980-01-01

    The transposon Tn10, coding for resistance to tetracycline, was inserted close to the tyrR+ gene at min 28 on the Escherichia coli chromosome. The homology between this transposon and a lambda (Tn10) phage was employed to direct integration of lambda close to tyrR+ with subsequent isolation of a lambda (Tn10) tyrR+ transducing phage. Results of restriction endonuclease analysis of the transducing phage are presented. Images PMID:6254949

  14. O acetylation of the enterobacterial common antigen polysaccharide is catalyzed by the product of the yiaH gene of Escherichia coli K-12.

    Science.gov (United States)

    Kajimura, Junko; Rahman, Arifur; Hsu, James; Evans, Matthew R; Gardner, Kevin H; Rick, Paul D

    2006-11-01

    The carbohydrate component of the enterobacterial common antigen (ECA) of Escherichia coli K-12 occurs primarily as a water-soluble cyclic polysaccharide located in the periplasm (ECA(CYC)) and as a phosphoglyceride-linked linear polysaccharide located on the cell surface (ECA(PG)). The polysaccharides of both forms are comprised of the amino sugars N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-mannosaminuronic acid (ManNAcA), and 4-acetamido-4,6-dideoxy-D-galactose (Fuc4NAc). These amino sugars are linked to one another to form trisaccharide repeat units with the structure -->3-alpha-D-Fuc4NAc-(1-->4)-beta-D-ManNAcA-(1-->4)-alpha-D-GlcNAc-(1-->. The hydroxyl group in the 6 position of the GlcNAc residues of both ECA(CYC) and ECA(PG) are nonstoichiometrically esterified with acetyl groups. Random transposon insertion mutagenesis of E. coli K-12 resulted in the generation of a mutant defective in the incorporation of O-acetyl groups into both ECA(CYC) and ECA(PG). This defect was found to be due to an insertion of the transposon into the yiaH locus, a putative gene of unknown function located at 80.26 min on the E. coli chromosomal map. Bioinformatic analyses of the predicted yiaH gene product indicate that it is an integral inner membrane protein that is a member of an acyltransferase family of enzymes found in a wide variety of organisms. The results of biochemical and genetic experiments presented here strongly support the conclusion that yiaH encodes the O-acetyltransferase responsible for the incorporation of O-acetyl groups into both ECA(CYC) and ECA(PG). Accordingly, we propose that this gene be designated wecH.

  15. Interaction of lead nitrate and cadmium chloride with Escherichia coli K-12 and Salmonella typhimurium global regulatory mutants.

    Science.gov (United States)

    LaRossa, R A; Smulski, D R; Van Dyk, T K

    1995-01-01

    To investigate the interactions of heavy metals with cells, a minimal medium for the growth of enteric bacteria using glycerol-2-phosphate as the sole phosphorus source was developed that avoided precipitation of Pb2+ with inorganic phosphate. Using this medium, spontaneous mutants of Escherichia coli resistant to addition of Pb(NO3)2 were isolated. Thirty-five independent mutants all conferred a low level of resistance. Disk diffusion assays on solid medium were used to survey the response of E. coli and Salmonella typhimurium mutants altered in global regulatory networks to Pb(NO3)2 and CdCl2. Strains bearing mutations in oxyR and rpoH were the most hypersensitive to these compounds. Based upon the response of strains completely devoid of isozymes needed to inactivate reactive oxygen species, this hypersensitivity to lead and cadmium is attributable to alteration in superoxide dismutase rather than catalase levels. Similar analysis of chaperone-defective mutants suggests that these metals damage proteins in vivo.

  16. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling

    Science.gov (United States)

    2013-01-01

    Background Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads. Results To fill these gaps, we have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM (http://bioinfolab.uncc.edu/TruHmm_package/) for assembling full length transcripts. We found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases. Conclusions As has been demonstrated in many other prokaryotes, E. coli K12 also has a highly complex and dynamic transcriptomes under different culture conditions and growth phases. Such complex and dynamic transcriptomes might play important roles in the physiology of the bacterium. TruHMM is a highly accurate and robust algorithm for assembling full-length transcripts in prokaryotes using directional RNA

  17. [Intra- and intermolecular recombination of test plasmids in K12 Escherichia coli cells carrying an RTF derivative of the R1drd-19 plasmid].

    Science.gov (United States)

    Terent'ev, M A; Chenin, L S

    1989-03-01

    The RTF derivative of the plasmid R1drd-19 was found to stimulate recombination of the tester plasmids in a recB mutant of Escherichia coli K12. The frequency of intramolecular recombination is increased 3.5 and 20-fold, as compared to the one in rec+ and rec- strains, respectively. The frequency of interplasmid recombination is enhanced 4 and 9-fold, respectively. Considerable heterogeneity of the recombination products of the tester plasmid intramolecular recombination in recB-/RTFR1-19 strain has been revealed. It is hypothesized that a "recombinase" encoded by Rldrd-19 plasmid determines a new minor pathway in recB- (Rec P) which differs in activity and, perhaps substrate specificity from the main Rec BCD pathway.

  18. RecA4142 Causes SOS Constitutive Expression by Loading onto Reversed Replication Forks in Escherichia coli K-12

    Science.gov (United States)

    Long, Jarukit Edward; Massoni, Shawn C.; Sandler, Steven J.

    2010-01-01

    Escherichia coli initiates the SOS response when single-stranded DNA (ssDNA) produced by DNA damage is bound by RecA and forms a RecA-DNA filament. recA SOS constitutive [recA(Con)] mutants induce the SOS response in the absence of DNA damage. It has been proposed that recA(Con) mutants bind to ssDNA at replication forks, although the specific mechanism is unknown. Previously, it had been shown that recA4142(F217Y), a novel recA(Con) mutant, was dependent on RecBCD for its high SOS constitutive [SOS(Con)] expression. This was presumably because RecA4142 was loaded at a double-strand end (DSE) of DNA. Herein, it is shown that recA4142 SOS(Con) expression is additionally dependent on ruvAB (replication fork reversal [RFR] activity only) and recJ (5′→3′ exonuclease), xonA (3′→5′ exonuclease) and partially dependent on recQ (helicase). Lastly, sbcCD mutations (Mre11/Rad50 homolog) in recA4142 strains caused full SOS(Con) expression in an ruvAB-, recBCD-, recJ-, and xonA-independent manner. It is hypothesized that RuvAB catalyzes RFR, RecJ and XonA blunt the DSE (created by the RFR), and then RecBCD loads RecA4142 onto this end to produce SOS(Con) expression. In sbcCD mutants, RecA4142 can bind other DNA substrates by itself that are normally degraded by the SbcCD nuclease. PMID:20304994

  19. RfaH suppresses small RNA MicA inhibition of fimB expression in Escherichia coli K-12.

    Science.gov (United States)

    Moores, Alexandra; Chipper-Keating, Saranna; Sun, Lei; McVicker, Gareth; Wales, Lynn; Gashi, Krishna; Blomfield, Ian C

    2014-01-01

    The phase variation (reversible on-off switching) of the type 1 fimbrial adhesin of Escherichia coli involves a DNA inversion catalyzed by FimB (switching in either direction) or FimE (on-to-off switching). Here, we demonstrate that RfaH activates expression of a FimB-LacZ protein fusion while having a modest inhibitory effect on a comparable fimB-lacZ operon construct and on a FimE-LacZ protein fusion, indicating that RfaH selectively controls fimB expression at the posttranscriptional level. Further work demonstrates that loss of RfaH enables small RNA (sRNA) MicA inhibition of fimB expression even in the absence of exogenous inducing stress. This effect is explained by induction of σ(E), and hence MicA, in the absence of RfaH. Additional work confirms that the procaine-dependent induction of micA requires OmpR, as reported previously (A. Coornaert et al., Mol. Microbiol. 76:467-479, 2010, doi:10.1111/j.1365-2958.2010.07115.x), but also demonstrates that RfaH inhibition of fimB transcription is enhanced by procaine independently of OmpR. While the effect of procaine on fimB transcription is shown to be independent of RcsB, it was found to require SlyA, another known regulator of fimB transcription. These results demonstrate a complex role for RfaH as a regulator of fimB expression.

  20. SlyA Protein Activates fimB Gene Expression and Type 1 Fimbriation in Escherichia coli K-12*

    Science.gov (United States)

    McVicker, Gareth; Sun, Lei; Sohanpal, Baljinder K.; Gashi, Krishna; Williamson, Richard A.; Plumbridge, Jacqueline; Blomfield, Ian C.

    2011-01-01

    We have demonstrated that SlyA activates fimB expression and hence type 1 fimbriation, a virulence factor in Escherichia coli. SlyA is shown to bind to two operator sites (OSA1 and OSA2), situated between 194 and 167 base pairs upstream of the fimB transcriptional start site. fimB expression is derepressed in an hns mutant and diminished by a slyA mutation in the presence of H-NS only. H-NS binds to multiple sites in the promoter region, including two sites (H-NS2 and H-NS3) that overlap OSA1 and OSA2, respectively. Mutations that disrupt either OSA1 or OSA2 eliminate or reduce the activating effect of SlyA but have different effects on the level of expression. We interpret these results as reflecting the relative competition between SlyA and H-NS binding. Moreover we show that SlyA is capable of displacing H-NS from its binding sites in vitro. We suggest SlyA binding prevents H-NS binding to H-NS2 and H-NS3 and the subsequent oligomerization of H-NS necessary for full inhibition of fimB expression. In addition, we show that SlyA activates fimB expression independently of two other known regulators of fimB expression, NanR and NagC. It is demonstrated that the rarely used UUG initiation codon limits slyA expression and that low SlyA levels limit fimB expression. Furthermore, Western blot analysis shows that cells grown in rich-defined medium contain ∼1000 SlyA dimers per cell whereas those grown in minimal medium contain >20% more SlyA. This study extends our understanding of the role that SlyA plays in the host-bacterial relationship. PMID:21768111

  1. SlyA protein activates fimB gene expression and type 1 fimbriation in Escherichia coli K-12.

    Science.gov (United States)

    McVicker, Gareth; Sun, Lei; Sohanpal, Baljinder K; Gashi, Krishna; Williamson, Richard A; Plumbridge, Jacqueline; Blomfield, Ian C

    2011-09-16

    We have demonstrated that SlyA activates fimB expression and hence type 1 fimbriation, a virulence factor in Escherichia coli. SlyA is shown to bind to two operator sites (O(SA1) and O(SA2)), situated between 194 and 167 base pairs upstream of the fimB transcriptional start site. fimB expression is derepressed in an hns mutant and diminished by a slyA mutation in the presence of H-NS only. H-NS binds to multiple sites in the promoter region, including two sites (H-NS2 and H-NS3) that overlap O(SA1) and O(SA2), respectively. Mutations that disrupt either O(SA1) or O(SA2) eliminate or reduce the activating effect of SlyA but have different effects on the level of expression. We interpret these results as reflecting the relative competition between SlyA and H-NS binding. Moreover we show that SlyA is capable of displacing H-NS from its binding sites in vitro. We suggest SlyA binding prevents H-NS binding to H-NS2 and H-NS3 and the subsequent oligomerization of H-NS necessary for full inhibition of fimB expression. In addition, we show that SlyA activates fimB expression independently of two other known regulators of fimB expression, NanR and NagC. It is demonstrated that the rarely used UUG initiation codon limits slyA expression and that low SlyA levels limit fimB expression. Furthermore, Western blot analysis shows that cells grown in rich-defined medium contain ~1000 SlyA dimers per cell whereas those grown in minimal medium contain >20% more SlyA. This study extends our understanding of the role that SlyA plays in the host-bacterial relationship.

  2. Loss of expression of cspC, a cold shock family gene, confers a gain of fitness in Escherichia coli K-12 strains.

    Science.gov (United States)

    Rath, Devashish; Jawali, Narendra

    2006-10-01

    The CspA family of cold shock genes in Escherichia coli K-12 includes nine paralogs, cspA to cspI. Some of them have been implicated in cold stress adaptation. Screening for mutations among common laboratory E. coli strains showed a high degree of genetic diversity in cspC but not in cspA and cspE. This diversity in cspC was due to a wide spectrum of variations including insertions of IS elements, deletion, and point mutation. Northern analysis of these mutants showed loss of cspC expression in all but one case. Further analysis of the loss-of-function cspC mutants showed that they have a fitness advantage in broth culture after 24 h over their isogenic wild-type derivatives. Conversely, introduction of mutated cspC alleles conferred a competitive fitness advantage to AB1157, a commonly used laboratory strain. This provides the evidence that loss of cspC expression is both necessary and sufficient to confer a gain of fitness as seen in broth culture over 24 h. Together, these results ascribe a novel role in cellular growth at 37 degrees C for CspC, a member of the cold shock domain-containing protein family.

  3. Escherichia coli K-12 survives anaerobic exposure at pH 2 without RpoS, Gad, or hydrogenases, but shows sensitivity to autoclaved broth products.

    Directory of Open Access Journals (Sweden)

    Daniel P Riggins

    Full Text Available Escherichia coli and other enteric bacteria survive exposure to extreme acid (pH 2 or lower in gastric fluid. Aerated cultures survive via regulons expressing glutamate decarboxylase (Gad, activated by RpoS, cyclopropane fatty acid synthase (Cfa and others. But extreme-acid survival is rarely tested under low oxygen, a condition found in the stomach and the intestinal tract. We observed survival of E. coli K-12 W3110 at pH 1.2-pH 2.0, conducting all manipulations (overnight culture at pH 5.5, extreme-acid exposure, dilution and plating in a glove box excluding oxygen (10% H2, 5% CO2, balance N2. With dissolved O2 concentrations maintained below 6 µM, survival at pH 2 required Cfa but did not require GadC, RpoS, or hydrogenases. Extreme-acid survival in broth (containing tryptone and yeast extract was diminished in media that had been autoclaved compared to media that had been filtered. The effect of autoclaved media on extreme-acid survival was most pronounced when oxygen was excluded. Exposure to H2O2 during extreme-acid treatment increased the death rate slightly for W3110 and to a greater extent for the rpoS deletion strain. Survival at pH 2 was increased in strains lacking the anaerobic regulator fnr. During anaerobic growth at pH 5.5, strains deleted for fnr showed enhanced transcription of acid-survival genes gadB, cfa, and hdeA, as well as catalase (katE. We show that E. coli cultured under oxygen exclusion (<6 µM O2 requires mechanisms different from those of aerated cultures. Extreme acid survival is more sensitive to autoclave products under oxygen exclusion.

  4. The genome sequence of E. coli W (ATCC 9637: comparative genome analysis and an improved genome-scale reconstruction of E. coli

    Directory of Open Access Journals (Sweden)

    Lee Sang

    2011-01-01

    Full Text Available Abstract Background Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637, one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses. Results We have sequenced and annotated the genome of E. coli W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp and pRK2 (5,360 bp, are also present. W has unique features relative to other sequenced laboratory strains (K-12, B and Crooks: it has a larger genome and belongs to phylogroup B1 rather than A. W also grows on a much broader range of carbon sources than does K-12. A genome-scale reconstruction was developed and validated in order to interrogate metabolic properties. Conclusions The genome of W is more similar to commensal and pathogenic B1 strains than phylogroup A strains, and therefore has greater utility for comparative analyses with these strains. W should therefore be the strain of choice, or 'type strain' for group B1 comparative analyses. The genome annotation and tools created here are expected to allow further utilization and development of E. coli W as an industrial organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction allow it to more accurately define E. coli metabolism relative to previous models.

  5. [The influence of Bordetella pertussis bvgAS operon on formation and resolution of plasmid-chromosome cointegrates in Escherichia coli K12 mutants with damages in common components of the phosphoenolpyruvate:sugar phosphotransferase system].

    Science.gov (United States)

    Umiarov, A M; Siniashina, L N; Amelina, I P; Datsenko, K A; Bol'shakova, T N; Dobrynina, O Iu; Karataev, G I

    2010-01-01

    The plasmids containing the genetically marked variants of Bordetela pertussi transposon TnBP were synthesized on the base of the plasmid with thermosensitive replication. The integration frequency of these plasmids into the E.coli K12 chromosome at non-permissive temperature (42 degrees C) was determined. It was found that the frequency of forming of RSBP-induced plasmid-chromosome cointegrated in bacteria E.coli K12 deficient in HPr or Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system was decreased. The bvgAS operon from B.pertussis in trans-position restores the ability of mutant E.coli K12 to form and resolve.

  6. Development of a new fluorescent reporter:operator system: location of AraC regulated genes in Escherichia coli K-12.

    Science.gov (United States)

    Sellars, Laura E; Bryant, Jack A; Sánchez-Romero, María-Antonia; Sánchez-Morán, Eugenio; Busby, Stephen J W; Lee, David J

    2017-08-03

    In bacteria, many transcription activator and repressor proteins regulate multiple transcription units that are often distally distributed on the bacterial genome. To investigate the subcellular location of DNA bound proteins in the folded bacterial nucleoid, fluorescent reporters have been developed which can be targeted to specific DNA operator sites. Such Fluorescent Reporter-Operator System (FROS) probes consist of a fluorescent protein fused to a DNA binding protein, which binds to an array of DNA operator sites located within the genome. Here we have developed a new FROS probe using the Escherichia coli MalI transcription factor, fused to mCherry fluorescent protein. We have used this in combination with a LacI repressor::GFP protein based FROS probe to assess the cellular location of commonly regulated transcription units that are distal on the Escherichia coli genome. We developed a new DNA binding fluorescent reporter, consisting of the Escherichia coli MalI protein fused to the mCherry fluorescent protein. This was used in combination with a Lac repressor:green fluorescent protein fusion to examine the spatial positioning and possible co-localisation of target genes, regulated by the Escherichia coli AraC protein. We report that induction of gene expression with arabinose does not result in co-localisation of AraC-regulated transcription units. However, measurable repositioning was observed when gene expression was induced at the AraC-regulated promoter controlling expression of the araFGH genes, located close to the DNA replication terminus on the chromosome. Moreover, in dividing cells, arabinose-induced expression at the araFGH locus enhanced chromosome segregation after replication. Regions of the chromosome regulated by AraC do not colocalise, but transcription events can induce movement of chromosome loci in bacteria and our observations suggest a role for gene expression in chromosome segregation.

  7. Genomic and Phenomic Study of Mammary Pathogenic Escherichia coli

    Science.gov (United States)

    Blum, Shlomo E.; Heller, Elimelech D.; Sela, Shlomo; Elad, Daniel; Edery, Nir; Leitner, Gabriel

    2015-01-01

    Escherichia coli is a major etiological agent of intra-mammary infections (IMI) in cows, leading to acute mastitis and causing great economic losses in dairy production worldwide. Particular strains cause persistent IMI, leading to recurrent mastitis. Virulence factors of mammary pathogenic E. coli (MPEC) involved pathogenesis of mastitis as well as those differentiating strains causing acute or persistent mastitis are largely unknown. This study aimed to identify virulence markers in MPEC through whole genome and phenome comparative analysis. MPEC strains causing acute (VL2874 and P4) or persistent (VL2732) mastitis were compared to an environmental strain (K71) and to the genomes of strains representing different E. coli pathotypes. Intra-mammary challenge in mice confirmed experimentally that the strains studied here have different pathogenic potential, and that the environmental strain K71 is non-pathogenic in the mammary gland. Analysis of whole genome sequences and predicted proteomes revealed high similarity among MPEC, whereas MPEC significantly differed from the non-mammary pathogenic strain K71, and from E. coli genomes from other pathotypes. Functional features identified in MPEC genomes and lacking in the non-mammary pathogenic strain were associated with synthesis of lipopolysaccharide and other membrane antigens, ferric-dicitrate iron acquisition and sugars metabolism. Features associated with cytotoxicity or intra-cellular survival were found specifically in the genomes of strains from severe and acute (VL2874) or persistent (VL2732) mastitis, respectively. MPEC genomes were relatively similar to strain K-12, which was subsequently shown here to be possibly pathogenic in the mammary gland. Phenome analysis showed that the persistent MPEC was the most versatile in terms of nutrients metabolized and acute MPEC the least. Among phenotypes unique to MPEC compared to the non-mammary pathogenic strain were uric acid and D-serine metabolism. This study

  8. First report on rapid screening of nanomaterial-based antimicrobial agents against β-lactamase resistance using pGLO plasmid transformed Escherichia coli HB 101 K-12

    Science.gov (United States)

    Raj, M. Alpha; Muralidhar, Y.; Sravanthi, M.; Prasad, T. N. V. K. V.; Nissipriya, M.; Reddy, P. Sirisha; Neelima, T. Shoba; Reddy, G. Dilip; Adilaxmamma, K.; Kumar, P. Anand; Krishna, T. Giridhara

    2016-08-01

    Combating antibiotic resistance requires discovery of novel antimicrobials effective against resistant bacteria. Herein, we present for the first time, pGLO plasmid transformed Escherichia coli HB 101 K 12 as novel model for screening of nanomaterial-based antimicrobial agents against β-lactamase resistance. E. coli HB 101 was transformed by pGLO plasmid in the presence of calcium chloride (50 mM; pH 6.1) aided by heat shock (0-42-0 °C). The transformed bacteria were grown on Luria-Bertani agar containing ampicillin (amp) and arabinose (ara). The transformed culture was able to grow in the presence of ampicillin and also exhibited fluorescence under UV light. Both untransformed and transformed bacteria were used for screening citrate-mediated nanosilver (CNS), aloin-mediated nanosilver (ANS), 11-α-keto-boswellic acid (AKBA)-mediated nanosilver (BNS); nanozinc oxide, nanomanganese oxide (NMO) and phytochemicals such as aloin and AKBA. Minimum inhibitory concentrations (MIC) were obtained by microplate method using ρ-iodo nitro tetrazolium indicator. All the compounds were effective against transformed bacteria except NMO and AKBA. Transformed bacteria exhibited reverse cross resistance against aloin. ANS showed the highest antibacterial activity with a MIC of 0.32 ppm followed by BNS (10.32 ppm), CNS (20.64 ppm) and NZO (34.83 ppm). Thus, pGLO plasmid can be used to induce resistance against β-lactam antibiotics and the model can be used for rapid screening of new antibacterial agents effective against resistant bacteria.

  9. Comparative study of time-dependent effects of 4 and 8 Hz mechanical vibration at infrasound frequency on E. coli K-12 cells proliferation.

    Science.gov (United States)

    Martirosyan, Varsik; Ayrapetyan, Sinerik

    2015-01-01

    The aim of the present work is to study the time-dependent effects of mechanical vibration (MV) at infrasound (IS) frequency at 4 and 8 Hz on E. coli K-12 growth by investigating the cell proliferation, using radioactive [(3)H]-thymidine assay. In our previous work it was suggested that the aqua medium can serve as a target through which the biological effect of MV on microbes could be realized. At the same time it was shown that microbes have mechanosensors on the surface of the cells and can sense small changes of the external environment. The obtained results were shown that the time-dependent effects of MV at 4 and 8 Hz frequency could either stimulate or inhibit the growth of microbes depending from exposure time. It more particularly, the invention relates to a method for controlling biological functions through the application of mechanical vibration, thus making it possible to artificially control the functions of bacterial cells, which will allow us to develop method that can be used in agriculture, industry, medicine, biotechnology to control microbial growth.

  10. The study of the effects of mechanical vibration at infrasound frequency on [(3)H]-thymidine incorporation into DNA of E. coli K-12.

    Science.gov (United States)

    Martirosyan, Varsik; Baghdasaryan, Naira; Ayrapetyan, Sinerik

    2013-03-01

    The aim of the present work was to investigate the frequency-dependent effects of mechanical vibration at infrasound frequency (MV at IS frequency or MV) on E. coli K-12 growth by investigating the cell proliferation, using radioactive [(3)H]-thymidine assay. The frequency-dependent effects of MV were shown that it could either stimulate or inhibit the growth of microbes. However, the mechanism through which the MV effects affect the bacterial cells is not clear yet. It was suggested that the aqua medium can serve as a target through which the biological effect of MV on microbes could be realized. To check this hypothesis the frequency-dependent effect (2, 4, 6, 8, 10 Hz) of MV on the bacterial growth in cases of exposure the preliminary treated microbes-free medium and microbes containing medium were studied. It has been shown that MV at 4, 8, and 10 Hz frequency has inhibition effects, while at 2 and 6 Hz has stimulation effects on cell proliferation.

  11. Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12

    Directory of Open Access Journals (Sweden)

    Radmacher Michael D

    2006-10-01

    Full Text Available Abstract Background In Escherichia coli, pH regulates genes for amino-acid and sugar catabolism, electron transport, oxidative stress, periplasmic and envelope proteins. Many pH-dependent genes are co-regulated by anaerobiosis, but the overall intersection of pH stress and oxygen limitation has not been investigated. Results The pH dependence of gene expression was analyzed in oxygen-limited cultures of E. coli K-12 strain W3110. E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Affymetrix array hybridization revealed pH-dependent expression of 1,384 genes and 610 intergenic regions. A core group of 251 genes showed pH responses similar to those in a previous study of cultures grown with aeration. The highly acid-induced gene yagU was shown to be required for extreme-acid resistance (survival at pH 2. Acid also up-regulated fimbriae (fimAC, periplasmic chaperones (hdeAB, cyclopropane fatty acid synthase (cfa, and the "constitutive" Na+/H+ antiporter (nhaB. Base up-regulated core genes for maltodextrin transport (lamB, mal, ATP synthase (atp, and DNA repair (recA, mutL. Other genes showed opposite pH responses with or without aeration, for example ETS components (cyo,nuo, sdh and hydrogenases (hya, hyb, hyc, hyf, hyp. A hypF strain lacking all hydrogenase activity showed loss of extreme-acid resistance. Under oxygen limitation only, acid down-regulated ribosome synthesis (rpl,rpm, rps. Acid up-regulated the catabolism of sugar derivatives whose fermentation minimized acid production (gnd, gnt, srl, and also a cluster of 13 genes in the gadA region. Acid up-regulated drug transporters (mdtEF, mdtL, but down-regulated penicillin-binding proteins (dacACD, mreBC. Intergenic regions containing regulatory sRNAs were up-regulated by acid (ryeA, csrB, gadY, rybC. Conclusion pH regulates a core set of genes independently of oxygen, including yagU, fimbriae, periplasmic chaperones, and nha

  12. Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63.

    Science.gov (United States)

    Kurakata, Yuma; Uechi, Akiko; Yoshida, Hiromi; Kamitori, Shigehiro; Sakano, Yoshiyuki; Nishikawa, Atsushi; Tonozuka, Takashi

    2008-08-01

    Proteins belonging to the glycoside hydrolase family 63 (GH63) are found in bacteria, archaea, and eukaryotes. Eukaryotic GH63 proteins are processing *-glucosidase I enzymes that hydrolyze an oligosaccharide precursor of eukaryotic N-linked glycoproteins. In contrast, the functions of the bacterial and archaeal GH63 proteins are unclear. Here we determined the crystal structure of a bacterial GH63 enzyme, Escherichia coli K12 YgjK, at 1.78 A resolution and investigated some properties of the enzyme. YgjK consists of the N-domain and the A-domain, joined by a linker region. The N-domain is composed of 18 antiparallel beta-strands and is classified as a super-beta-sandwich. The A-domain contains 16 *-helices, 12 of which form an (*/*)(6)-barrel; the remaining 4 *-helices are found in an extra structural unit that we designated as the A'-region. YgjK, a member of the glycoside hydrolase clan GH-G, shares structural similarity with glucoamylase (GH15) and chitobiose phosphorylase (GH94) [corrected] both of which belong to clan GH-L or GH-L-like [corrected] In crystal structures of YgjK in complex with glucose, mannose, and galactose, all of the glucose, mannose, and galactose units were located in the catalytic cleft. YgjK showed the highest activity for the *-1,3-glucosidic linkage of nigerose, but also hydrolyzed trehalose, kojibiose, and maltooligosaccharides from maltose to maltoheptaose, although the activities were low. These findings suggest that YgjK is a glucosidase with relaxed specificity for sugars.

  13. Whole Genome Epidemiological Typing of Escherichia coli

    DEFF Research Database (Denmark)

    Kaas, Rolf Sommer

    Escherichia coli (E. coli) is of huge importance in global health both as a commensal organism living within its host or as a pathogen causing millions of infections each year. Infections occur both sporadic and as outbreaks with sometimes up to thousands of infected people. To limit the number...... of infections it is important to monitor pathogenic E. coli in order to detect outbreaks as quickly as possible and find the source of the outbreak. The effectiveness of monitoring and tracking of pathogens is very dependent on the typing methods that are employed. Classical typing methods employed for E. coli......D thesis attempts to take the first steps toward such a method. In Kaas I all publicly available E. coli genomes sequenced (186) are analyzed. 1,702 core genes were found in all genomes. 3,051 genes were found in 95% of the genomes. The pan genome was found to consist of 16,373 genes. The overall phylogeny...

  14. Structural Basis for Substrate Specificity in Phosphate Binding (beta/alpha)8-Barrels: D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K-12

    Energy Technology Data Exchange (ETDEWEB)

    Chan,K.; Fedorov, A.; Almo, S.; Gerlt, J.

    2008-01-01

    Enzymes that share the ({beta}/{alpha})8-barrel fold catalyze a diverse range of reactions. Many utilize phosphorylated substrates and share a conserved C-terminal ({beta}/a)2-quarter barrel subdomain that provides a binding motif for the dianionic phosphate group. We recently reported functional and structural studies of d-ribulose 5-phosphate 3-epimerase (RPE) from Streptococcus pyogenes that catalyzes the equilibration of the pentulose 5-phosphates d-ribulose 5-phosphate and d-xylulose 5-phosphate in the pentose phosphate pathway [J. Akana, A. A. Fedorov, E. Fedorov, W. R. P. Novack, P. C. Babbitt, S. C. Almo, and J. A. Gerlt (2006) Biochemistry 45, 2493-2503]. We now report functional and structural studies of d-allulose 6-phosphate 3-epimerase (ALSE) from Escherichia coli K-12 that catalyzes the equilibration of the hexulose 6-phosphates d-allulose 6-phosphate and d-fructose 6-phosphate in a catabolic pathway for d-allose. ALSE and RPE prefer their physiological substrates but are promiscuous for each other's substrate. The active sites (RPE complexed with d-xylitol 5-phosphate and ALSE complexed with d-glucitol 6-phosphate) are superimposable (as expected from their 39% sequence identity), with the exception of the phosphate binding motif. The loop following the eighth {beta}-strand in ALSE is one residue longer than the homologous loop in RPE, so the binding site for the hexulose 6-phosphate substrate/product in ALSE is elongated relative to that for the pentulose 5-phosphate substrate/product in RPE. We constructed three single-residue deletion mutants of the loop in ALSE, ?T196, ?S197 and ?G198, to investigate the structural bases for the differing substrate specificities; for each, the promiscuity is altered so that d-ribulose 5-phosphate is the preferred substrate. The changes in kcat/Km are dominated by changes in kcat, suggesting that substrate discrimination results from differential transition state stabilization. In both ALSE and RPE, the

  15. First international E. coli genome meeting

    Energy Technology Data Exchange (ETDEWEB)

    1992-12-31

    This volume is a collection of abstracts of oral presentations and poster sessions of studies reported at the First International E. Coli Genome Meeting, held September 10-14, 1992 at the University of Wisconsin.

  16. First international E. coli genome meeting

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    This volume is a collection of abstracts of oral presentations and poster sessions of studies reported at the First International E. Coli Genome Meeting, held September 10-14, 1992 at the University of Wisconsin.

  17. Third International E. coli genome meeting

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    Proceedings of the Third E. Coli Genome Meeting are provided. Presentations were divided into sessions entitled (1) Large Scale Sequencing, Sequence Analysis; (2) Databases; (3) Sequence Analysis; (4) Sequence Divergence in E. coli Strains; (5) Repeated Sequences and Regulatory Motifs; (6) Mutations, Rearrangements and Stress Responses; and (7) Origins of New Genes. The document provides a collection of abstracts of oral and poster presentations.

  18. An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth.

    Science.gov (United States)

    Zhao, G; Winkler, M E

    1994-01-01

    We show that a tktA tktB double mutant, which is devoid of the two known transketolase isoenzymes of Escherichia coli K-12, requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth. This pyridoxine requirement can also be satisfied by 4-hydroxy-L-threonine or glycolaldehyde. These results provide direct evidence that D-erythrose-4-phosphate is a precursor of the pyridine ring of pyridoxine. In addition, they show that the two major E. coli transketolase isoenzymes are not required for the biosynthesis of D-1-deoxyxylulose, which is thought to be another precursor of pyridoxine. PMID:7928977

  19. An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth.

    OpenAIRE

    Zhao, G; Winkler, M E

    1994-01-01

    We show that a tktA tktB double mutant, which is devoid of the two known transketolase isoenzymes of Escherichia coli K-12, requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth. This pyridoxine requirement can also be satisfied by 4-hydroxy-L-threonine or glycolaldehyde. These results provide direct evidence that D-erythrose-4-phosphate is a precursor of the pyridine ring of pyridoxine. In addition, they show that the two major E. coli transketolase iso...

  20. Impact of metal ion homeostasis of genetically modified Escherichia coli Nissle 1917 and K12 (W3110) strains on colonization properties in the murine intestinal tract

    OpenAIRE

    Kupz, Andreas; Fischer, André; Nies, Dietrich H.; Grass, Gregor; Göbel, Ulf B.; Bereswill, Stefan; Heimesaat, Markus M.

    2013-01-01

    Metal ions are integral parts of pro- as well as eukaryotic cell homeostasis. Escherichia coli proved a valuable in vitro model organism to elucidate essential mechanisms involved in uptake, storage, and export of metal ions. Given that E. coli Nissle 1917 is able to overcome murine colonization resistance, we generated several E. coli Nissle 1917 mutants with defects in zinc, iron, copper, nickel, manganese homeostasis and performed a comprehensive survey of the impact of m...

  1. H-NS mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO

    OpenAIRE

    Westra, Edze Rients; Pul, Ümit; Heidrich, Nadja; Jore, Matthijs Miklas; Lundgren, Magnus; Stratmann, Thomas; Wurm, Reinhild; Raine, Amanda; Mescher, Melina; Heereveld, Luc Van; Mastop, Marieke; Wagner, E. Gerhart H.; Schnetz, Karin; Van Der Oost, John; Wagner, Rolf

    2010-01-01

    Abstract The recently discovered prokaryotic CRISPR/Cas defense system provides immunity against viral infections and plasmid conjugation. It has been demonstrated that in Escherichia coli transcription of the Cascade genes (casABCDE) and to some extent the CRISPR array, is repressed by heat-stable nucleoid-structuring (H-NS) protein, a global transcriptional repressor. Here we elaborate on the control of the E. coli CRISPR/Cas system, and study the effect on CRISPR-based anti-vira...

  2. Genome-wide profiling of histone modifications (H3K9me2 and H4K12ac) and gene expression in rust (uromyces appendiculatus) inoculated common bean (Phaseolus vulgaris L)

    OpenAIRE

    Ayyappan, Vasudevan; Kalavacharla, Venu (Kal); Thimmapuram, Jyothi; Bhide, Ketaki P; Sripathi, Venkateswara R.

    2015-01-01

    Histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. Genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. We report the genome-wide profiling of histone methylation (H3K9me2) and acetylation (H4K12ac) in common bean (Phaseolus vulgaris L.) under rust (Uromyces appendiculatus) stress using two high-throughput approaches, chromatin immunoprecipitation s...

  3. H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO

    NARCIS (Netherlands)

    Westra, E.R.; Pul, Ü.; Heidrich, N.; Jore, M.M.; Lundgren, N.M.J.; Stratmann, T.; Wurm, R.; Raine, A.; Mescher, M.; Heereveld, van L.; Mastop, M.; Wagner, E.G.H.; Schnetz, K.; Oost, van der J.; Wagner, R.; Brouns, S.J.J.

    2010-01-01

    The recently discovered prokaryotic CRISPR/Cas defence system provides immunity against viral infections and plasmid conjugation. It has been demonstrated that in Escherichia coli transcription of the Cascade genes (casABCDE) and to some extent the CRISPR array is repressed by heat-stable

  4. Effect of heat and radio frequency electric field treatments on membrane damage and intracellular leakage of UV-substances of Escherichia coli K-12 in apple juice

    Science.gov (United States)

    The need for a nonthermal intervention technology that can achieve microbial safety without altering nutritional quality of liquid foods led to the development of the radio frequency electric fields (RFEF) process. Previously, we documented formation of surface blebs on Escherichia coli cells treate...

  5. [Population genomic researches of Escherichia coli].

    Science.gov (United States)

    Wu, Y R; Yang, R F; Cui, Y J

    2016-06-01

    Population genomics, an interdiscipline of genomics and population genetics, is booming in recent years with the rapid growth number of deciphered genomes and revolutionizes the understanding of bacterial population diversity and evolution dynamics. It also largely improves the prevention and control of infectious disease through providing more accurate genotyping and source-tracing results and more comprehensive characteristics of emerging pathogens. In this review, taking one of the best characterized bacteria, Escherichia coli, as model, we reviewed the phylogenetic relationship across its five major populations (designated A, B1, B2, D and E); and summarized researches on molecular mutation rate, selection signals, and patterns of adaptive evolution. We also described the application of population genomics in responding against large-scale outbreaks of E. coli O157:H7 and E. coli O104:H4. These results indicated that, although being a novel discipline, population genomics has played an important role in deciphering bacterial population structures, exploring evolutionary patterns and combating emerging infectious diseases.

  6. A putrescine-inducible pathway comprising PuuE-YneI in which gamma-aminobutyrate is degraded into succinate in Escherichia coli K-12.

    Science.gov (United States)

    Kurihara, Shin; Kato, Kenji; Asada, Kei; Kumagai, Hidehiko; Suzuki, Hideyuki

    2010-09-01

    Gamma-aminobutyrate (GABA) is metabolized to succinic semialdehyde by GABA aminotransferase (GABA-AT), and the succinic semialdehyde is subsequently oxidized to succinate by succinic semialdehyde dehydrogenase (SSADH). In Escherichia coli, there are duplicate GABA-ATs (GabT and PuuE) and duplicate SSADHs (GabD and YneI). While GabT and GabD have been well studied previously, the characterization and expression analysis of PuuE and YneI are yet to be investigated. By analyzing the amino acid profiles in cells of DeltapuuE and/or DeltagabT mutants, this study demonstrated that PuuE plays an important role in GABA metabolism in E. coli cells. The similarity of the amino acid sequences of PuuE and GabT is 67.4%, and it was biochemically demonstrated that the catalytic center of GabT is conserved as an amino acid residue important for the enzymatic activity in PuuE as Lys-247. However, the regulation of expression of PuuE is significantly different from that of GabT. PuuE is induced by the addition of putrescine to the medium and is repressed by succinate and low aeration conditions; in contrast, GabT is almost constitutive. Similarly, YneI is induced by putrescine, while GabD is not. For E. coli, PuuE is important for utilization of putrescine as a sole nitrogen source and both PuuE and YneI are important for utilization of putrescine as a sole carbon source. The results demonstrate that the PuuE-YneI pathway was a putrescine-inducible GABA degradation pathway for utilizing putrescine as a nutrient source.

  7. A Putrescine-Inducible Pathway Comprising PuuE-YneI in Which γ-Aminobutyrate Is Degraded into Succinate in Escherichia coli K-12

    Science.gov (United States)

    Kurihara, Shin; Kato, Kenji; Asada, Kei; Kumagai, Hidehiko; Suzuki, Hideyuki

    2010-01-01

    γ-Aminobutyrate (GABA) is metabolized to succinic semialdehyde by GABA aminotransferase (GABA-AT), and the succinic semialdehyde is subsequently oxidized to succinate by succinic semialdehyde dehydrogenase (SSADH). In Escherichia coli, there are duplicate GABA-ATs (GabT and PuuE) and duplicate SSADHs (GabD and YneI). While GabT and GabD have been well studied previously, the characterization and expression analysis of PuuE and YneI are yet to be investigated. By analyzing the amino acid profiles in cells of ΔpuuE and/or ΔgabT mutants, this study demonstrated that PuuE plays an important role in GABA metabolism in E. coli cells. The similarity of the amino acid sequences of PuuE and GabT is 67.4%, and it was biochemically demonstrated that the catalytic center of GabT is conserved as an amino acid residue important for the enzymatic activity in PuuE as Lys-247. However, the regulation of expression of PuuE is significantly different from that of GabT. PuuE is induced by the addition of putrescine to the medium and is repressed by succinate and low aeration conditions; in contrast, GabT is almost constitutive. Similarly, YneI is induced by putrescine, while GabD is not. For E. coli, PuuE is important for utilization of putrescine as a sole nitrogen source and both PuuE and YneI are important for utilization of putrescine as a sole carbon source. The results demonstrate that the PuuE-YneI pathway was a putrescine-inducible GABA degradation pathway for utilizing putrescine as a nutrient source. PMID:20639325

  8. Overproduction, purification and structural characterization of the functional N-terminal DNA-binding domain of the fru repressor from Escherichia coli K-12.

    Science.gov (United States)

    Scarabel, M; Penin, F; Bonod-Bidaud, C; Nègre, D; Cozzone, A J; Cortay, J C

    1995-02-03

    A DNA fragment encoding the DNA-binding domain (amino acids 1-60) of the Escherichia coli fru transcriptional regulator was cloned into the pGEX-KT vector and expressed in frame with the fused gene encoding glutathione S-transferase. The fusion protein was purified to homogeneity by affinity chromatography on immobilized glutathione, and then cleaved with thrombin. After separation by a cation-exchange chromatography step, the DNA-binding domain exhibited proper folding, as shown by proton NMR analysis. Furthermore, it showed specific interaction with the operator region of the ace operon, as checked by gel retardation and DNA methylation-protection experiments.

  9. The CytR repressor antagonizes cyclic AMP-cyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12

    DEFF Research Database (Denmark)

    Søgaard-Andersen, Lotte; Martinussen, J; Møllegaard, N E

    1990-01-01

    We have investigated the regulation of the Escherichia coli deoCp2 promoter by the CytR repressor and the cyclic AMP (cAMP) receptor protein (CRP) complexed to cAMP. Promoter regions controlled by these two proteins characteristically contain tandem cAMP-CRP binding sites. Here we show that (i) Cyt......AMP-CRP complex; (iii) introduction of point mutations in either CRP target resulted in loss of CytR regulation; and (iv) regulation by CytR of deletion mutants lacking CRP-2 could be specifically reestablished by increasing the intracellular concentration of CytR. These findings indicate that both CRP targets...

  10. A novel putrescine importer required for type 1 pili-driven surface motility induced by extracellular putrescine in Escherichia coli K-12.

    Science.gov (United States)

    Kurihara, Shin; Suzuki, Hideyuki; Oshida, Mayu; Benno, Yoshimi

    2011-03-25

    Recently, many studies have reported that polyamines play a role in bacterial cell-to-cell signaling processes. The present study describes a novel putrescine importer required for induction of type 1 pili-driven surface motility. The surface motility of the Escherichia coli ΔspeAB ΔspeC ΔpotABCD strain, which cannot produce putrescine and cannot import spermidine from the medium, was induced by extracellular putrescine. Introduction of the gene deletions for known polyamine importers (ΔpotE, ΔpotFGHI, and ΔpuuP) or a putative polyamine importer (ΔydcSTUV) into the ΔspeAB ΔspeC ΔpotABCD strain did not affect putrescine-induced surface motility. The deletion of yeeF, an annotated putative putrescine importer, in the ΔspeAB ΔspeC ΔpotABCD ΔydcSTUV strain abolished surface motility in putrescine-supplemented medium. Complementation of yeeF by a plasmid vector restored surface motility. The surface motility observed in the present study was abolished by the deletion of fimA, suggesting that the surface motility is type 1 pili-driven. A transport assay using the yeeF(+) or ΔyeeF strains revealed that YeeF is a novel putrescine importer. The K(m) of YeeF (155 μM) is 40 to 300 times higher than that of other importers reported previously. On the other hand, the V(max) of YeeF (9.3 nmol/min/mg) is comparable to that of PotABCD, PotFGHI, and PuuP. The low affinity of YeeF for putrescine may allow E. coli to sense the cell density depending on the concentration of extracellular putrescine.

  11. A Novel Putrescine Importer Required for Type 1 Pili-driven Surface Motility Induced by Extracellular Putrescine in Escherichia coli K-12*

    Science.gov (United States)

    Kurihara, Shin; Suzuki, Hideyuki; Oshida, Mayu; Benno, Yoshimi

    2011-01-01

    Recently, many studies have reported that polyamines play a role in bacterial cell-to-cell signaling processes. The present study describes a novel putrescine importer required for induction of type 1 pili-driven surface motility. The surface motility of the Escherichia coli ΔspeAB ΔspeC ΔpotABCD strain, which cannot produce putrescine and cannot import spermidine from the medium, was induced by extracellular putrescine. Introduction of the gene deletions for known polyamine importers (ΔpotE, ΔpotFGHI, and ΔpuuP) or a putative polyamine importer (ΔydcSTUV) into the ΔspeAB ΔspeC ΔpotABCD strain did not affect putrescine-induced surface motility. The deletion of yeeF, an annotated putative putrescine importer, in the ΔspeAB ΔspeC ΔpotABCD ΔydcSTUV strain abolished surface motility in putrescine-supplemented medium. Complementation of yeeF by a plasmid vector restored surface motility. The surface motility observed in the present study was abolished by the deletion of fimA, suggesting that the surface motility is type 1 pili-driven. A transport assay using the yeeF+ or ΔyeeF strains revealed that YeeF is a novel putrescine importer. The Km of YeeF (155 μm) is 40 to 300 times higher than that of other importers reported previously. On the other hand, the Vmax of YeeF (9.3 nmol/min/mg) is comparable to that of PotABCD, PotFGHI, and PuuP. The low affinity of YeeF for putrescine may allow E. coli to sense the cell density depending on the concentration of extracellular putrescine. PMID:21266585

  12. The organization of the fuc regulon specifying L-fucose dissimilation in Escherichia coli K12 as determined by gene cloning.

    Science.gov (United States)

    Chen, Y M; Zhu, Y; Lin, E C

    1987-12-01

    In Escherichia coli the six known genes specifying the utilization of L-fucose as carbon and energy source cluster at 60.2 min and constitute a regulon. These genes include fucP (encoding L-fucose permease), fucI (encoding L-fucose isomerase), fucK (encoding L-fuculose kinase), fucA (encoding L-fuculose 1-phosphate aldolase), fucO (encoding L-1,2-propanediol oxidoreductase), and fucR (encoding the regulatory protein). In this study the fuc genes were cloned and their positions on the chromosome were established by restriction endonuclease and complementation analyses. Clockwise, the gene order is: fucO-fucA-fucP-fucI-fucK-fucR. The operons comprising the structural genes and the direction of transcription were determined by complementation analysis and Southern blot hybridization. The fucPIK and fucA operons are transcribed clockwise. The fucO operon is transcribed counterclockwise. The fucR gene product activates the three structural operons in trans.

  13. Simultaneous substitution of Gly96 to Ala and Ala183 to Thr in 5-enolpyruvylshikimate-3-phosphate synthase gene of E. coli (k12) and transformation of rapeseed (Brassica napus L.) in order to make tolerance to glyphosate.

    Science.gov (United States)

    Kahrizi, Danial; Salmanian, Ali Hatef; Afshari, Afsoon; Moieni, Ahmad; Mousavi, Amir

    2007-01-01

    Glyphosate is a non-selective broad-spectrum herbicide that inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). This is a key enzyme in the aromatic amino acid biosynthesis pathway of microorganisms and plants. The manipulation of bacterial EPSPS gene in order to reduce its affinity for glyphosate, followed by its transfer to plants is one of the most effective approaches for the production of glyphosate-tolerant plants. In this study, we chose to focus on amino acid residues glycine96 and alanine183 of the E. coli (k12) EPSPS enzyme. These two amino acids are important residues for glyphosate binding. We used site directed mutagenesis (SDM) to induce point mutations in the E. coli EPSPS gene, in order to convert glycine96 to alanine (Gly96Ala) and alanine183 to threonine (Ala183Thr). After confirming the mutation by sequencing, the altered EPSPS gene was transferred to rapeseed (Brassica napus L.) via Agrobacterium-mediated transformation. The transformed explants were screened in shoot induction medium containing 25 mg L-1 kanamycin. Glyphosate tolerance was assayed in putative transgenic plants. Statistical analysis of data showed that there was a significant difference between the transgenic and control plants. It was observed that transgenic plants were resistant to glyphosate at a concentration of 10 mM whereas the non-transformed control plants were unable to survive 1 mM glyphosate. The presence and copy numbers of the transgene were confirmed with PCR and Southern blotting analysis, respectively.

  14. Efficacy of a novel sanitizer composed of lactic acid and peroxyacetic acid against single strains of nonpathogenic Escherichia coli K-12, Listeria innocua, and Lactobacillus plantarum in aqueous solution and on surfaces of romaine lettuce and spinach.

    Science.gov (United States)

    Grace Ho, Kai-Lai; Luzuriaga, Diego A; Rodde, Kenneth M; Tang, Shannon; Phan, Cuong

    2011-09-01

    A novel sanitizer composed of lactic acid and peroxyacetic acid (LA-PAA) was developed as an alternative to chlorinated water (CW) for fresh produce processing. Single strains of Lactobacillus plantarum, nonpathogenic Escherichia coli K-12, and Listeria innocua were used to demonstrate the microbial efficacy of LA-PAA. LA-PAA achieved a >7.8-log reduction of L. innocua and L. plantarum suspended in water at 4°C for 20 s, and LA, PAA, and CW achieved reductions of 0.4, 4.8, and 2.7 log, respectively. LA-PAA, when compared with LA, PAA, and CW, enhanced the reduction of L. innocua attached to romaine leaves by >2.2 log, and improved the removal of E. coli attached to spinach leaves by >2.4 log. The exponential improvement in the microbial efficacy of LA-PAA showed synergism between LA and PAA. LA-PAA microbial efficacy was inversely proportional to pH value and directly correlated with residence time and concentration. Despite an improvement in microbial reduction through the addition of surfactant to LA-PAA, the usage of surfactant in washing fresh produce was impeded by excessive foaming during actual processing. Effects of organic matter on the performance of LA-PAA were minimal. External sensory evaluations showed that LA-PAA had no negative effects on the quality of lettuce and tender leaves. Temperature-abuse studies demonstrated that LA-PAA reduced decay by ∼50% when compared with CW. Overall, these results support the premise that LA-PAA has significant potential to be an alternative to CW for fresh produce processing.

  15. High-level expression of a bacterial laccase, CueO from Escherichia coli K12 in Pichia pastoris GS115 and its application on the decolorization of synthetic dyes.

    Science.gov (United States)

    Ma, Xiaojian; Liu, Lu; Li, Qingqing; Liu, Yunyun; Yi, Li; Ma, Lixin; Zhai, Chao

    2017-08-01

    Laccases are oxidoreductase catalyze the oxidation of a wide range of substrates with oxygen as the electron acceptor. This report was aimed to the high-level expression of a laccase, CueO from Escherichia coli K12 in Pichia pastoris GS115 and its application on decolorization of synthetic dyes. The yacK gene coding CueO was cloned into an expression vector of Pichia pastoris, pHBM905BDM and expressed in a secretory form with Pichia pastoris GS115 as the host. The yield of the recombinant protein was 556mg/L with high-density fermentation and the enzyme activity was about 41,000U/L. The recombinant laccase was purified and characterized. Its optimum pH and temperature was 3.0 and 55°C with 2, 2'-azino-bis-(3-ethylbenzothazoline-6-sulfonic acid) (ABTS) as the substrate, respectively. This recombinant protein was thermostable and its half life at 70°C was about 60min. In the presence of natural redox mediator acetosyringone, the purified recombinant laccase decolorized 98.1% and 98.5% of Congo red, malachite green, respectively. It also decolorized 90.03% of Remazol brilliant blue R without this mediator. In addition, this enzyme was applied on the decolorization of wastewater from a textile printing factory and showed an obvious bleaching effect. Copyright © 2017. Published by Elsevier Inc.

  16. Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

    Science.gov (United States)

    Skippington, Elizabeth; Ragan, Mark A.

    2012-01-01

    Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. Most sRNAs act by base pairing with a target mRNA, modulating its translation and/or stability; many of these RNAs share only limited complementarity to their mRNA target, and require the chaperone Hfq to facilitate base pairing. Little is known about the evolutionary dynamics of bacterial sRNAs. Here, we apply phylogenetic and network analyses to investigate the evolutionary processes and principles that govern sRNA gene distribution in 27 E. coli and Shigella genomes. We identify core (encoded in all 27 genomes) and variable sRNAs; more than two-thirds of the E. coli K-12 MG1655 sRNAs are core, whereas the others show patterns of presence and absence that are principally due to genetic loss, not duplication or lateral genetic transfer. We present evidence that variable sRNAs are less tightly integrated into cellular genetic regulatory networks than are the core sRNAs, and that Hfq facilitates posttranscriptional cross talk between the E. coli–Shigella core and variable genomes. Finally, we present evidence that more than 80% of genes targeted by Hfq-associated core sRNAs have been transferred within the E. coli–Shigella clade, and that most of these genes have been transferred intact. These results suggest that Hfq and sRNAs help integrate laterally acquired genes into established regulatory networks. PMID:22223756

  17. Classifying K-12 Blended Learning

    Science.gov (United States)

    Staker, Heather; Horn, Michael B.

    2012-01-01

    The growth of online learning in the K-12 sector is occurring both remotely through virtual schools and on campuses through blended learning. In emerging fields, definitions are important because they create a shared language that enables people to talk about the new phenomena. The blended-learning taxonomy and definitions presented in this paper…

  18. California's Future: K-12 Education

    Science.gov (United States)

    Hill, Laura; Gao, Niu; Warren, Paul

    2015-01-01

    California educates more than six million children in its K-12 public schools. More than half of these children are economically disadvantaged, and almost a quarter are not native English speakers (compared to less than one in ten nationwide). California is working to address these challenges, in part by adopting a new, simplified school finance…

  19. Complete Genome Sequence of Escherichia coli Strain WG5

    DEFF Research Database (Denmark)

    Imamovic, Lejla; Misiakou, Maria-Anna; van der Helm, Eric

    2018-01-01

    Escherichia coli strain WG5 is a widely used host for phage detection, including somatic coliphages employed as standard ISO method 10705-1 (2000). Here, we present the complete genome sequence of a commercial E. coli WG5 strain.......Escherichia coli strain WG5 is a widely used host for phage detection, including somatic coliphages employed as standard ISO method 10705-1 (2000). Here, we present the complete genome sequence of a commercial E. coli WG5 strain....

  20. Genome analysis of E. coli isolated from Crohn's disease patients.

    Science.gov (United States)

    Rakitina, Daria V; Manolov, Alexander I; Kanygina, Alexandra V; Garushyants, Sofya K; Baikova, Julia P; Alexeev, Dmitry G; Ladygina, Valentina G; Kostryukova, Elena S; Larin, Andrei K; Semashko, Tatiana A; Karpova, Irina Y; Babenko, Vladislav V; Ismagilova, Ruzilya K; Malanin, Sergei Y; Gelfand, Mikhail S; Ilina, Elena N; Gorodnichev, Roman B; Lisitsyna, Eugenia S; Aleshkin, Gennady I; Scherbakov, Petr L; Khalif, Igor L; Shapina, Marina V; Maev, Igor V; Andreev, Dmitry N; Govorun, Vadim M

    2017-07-19

    Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.

  1. Implication of the E. coli K12 uvrA and recA genes in the repair of 8-methoxypsoralen-induced mono adducts and crosslinks on plasmid DNA; Implicacion de los genes uvrA de E. coli K12 en la reparacion de monoaductos y entrecruzamien tos inducidos en DNA plasmidico por 8-metoxipso raleno mas luz ultravioleta A

    Energy Technology Data Exchange (ETDEWEB)

    Paramio, J.M.; Bauluz, C.; Vidania, R. de

    1986-07-01

    Genotoxicity of psoralen damages on plasmid DNA has been studied. pBR322 DNA was randomly modified with several concentrations of 8-methoxypsoralen plus 365 nm-UV light. After transformation into E. coli strains (wild-type, uvrA and recA) plasmid survival and mutagenesis were analyzed. To study the influence of the SOS response on plasmid recovery, preirradiation of the cells was performed. In absence of cell preirradiation, crosslinks were not repaired in any strain. Mono adducts were also lethal but in part removed by the excision-repair pathway. Preirradiation of the cells significantly. increased plasmid recovery in recA+ celia. In uvrA- only the mutagenic pathway seemed to be involved in the repair of the damaged DNA. Wild type strain showed the highest increase in plasmid survival, involving the repair of mono adducts and some fraction of crosslinks mainly through an error-free repair pathway. This suggests an enhancement of the excision repair promoted by the induction of SOS functions. (Author) 32 refs.

  2. Sigma factors in a thousand E. coli genomes

    DEFF Research Database (Denmark)

    Cook, Helen Victoria; Ussery, David

    2013-01-01

    , 2013), only less than half (983) are of sufficient quality to use in comparative genomic work. Unfortunately, even some of the ‘complete’ E. coli genomes are in pieces, and a few ‘draft’ genomes are good quality. Six of the seven known sigma factors in E. coli strain K‐12 are extremely well conserved......; the iron‐regulating sigma factor FecI (σ19) is missing in most genomes. Surprisingly, the E. coli strain CFT073 genome does not encode a functional RpoD (σ70), which is obviously essential, and this is likely due to poor genome assembly/annotation. We find a possible novel sigma factor present in more than...

  3. Genomic Comparative Study of Bovine Mastitis Escherichia coli

    Science.gov (United States)

    Kempf, Florent; Slugocki, Cindy; Blum, Shlomo E.; Leitner, Gabriel; Germon, Pierre

    2016-01-01

    Escherichia coli, one of the main causative agents of bovine mastitis, is responsible for significant losses on dairy farms. In order to better understand the pathogenicity of E. coli mastitis, an accurate characterization of E. coli strains isolated from mastitis cases is required. By using phylogenetic analyses and whole genome comparison of 5 currently available mastitis E. coli genome sequences, we searched for genotypic traits specific for mastitis isolates. Our data confirm that there is a bias in the distribution of mastitis isolates in the different phylogenetic groups of the E. coli species, with the majority of strains belonging to phylogenetic groups A and B1. An interesting feature is that clustering of strains based on their accessory genome is very similar to that obtained using the core genome. This finding illustrates the fact that phenotypic properties of strains from different phylogroups are likely to be different. As a consequence, it is possible that different strategies could be used by mastitis isolates of different phylogroups to trigger mastitis. Our results indicate that mastitis E. coli isolates analyzed in this study carry very few of the virulence genes described in other pathogenic E. coli strains. A more detailed analysis of the presence/absence of genes involved in LPS synthesis, iron acquisition and type 6 secretion systems did not uncover specific properties of mastitis isolates. Altogether, these results indicate that mastitis E. coli isolates are rather characterized by a lack of bona fide currently described virulence genes. PMID:26809117

  4. The Metamorphosis by K. (12)

    CERN Multimedia

    CERN Bulletin

    2012-01-01

    In the last issue of the Bulletin we reported on the first run of the new NA62 experiment. In this issue, we go behind the scenes to take a look at the production of the experiment's new kaon beam.   The start of the K12 beam line as seen during the installation of the shielding. 10-2, 10-3, 10-4, 10-5, 10-6 mbar… send in the protons! Since Thursday 1 November, the P42 beam line of the SPS has once again been sending protons to the beryllium target to produce the K12 kaon beam line eagerly awaited by the NA62 collaboration. This was no trivial matter! The first step was to clear the decks by dismantling the entire H10 beam line and NA60 experiment, as well as most of the NA48 experiment - representing some 1000 tonnes of equipment in total! Next came the complete renovation of the infrastructure, which dated back to 1979. The operation called on the expertise of virtually all branches of the EN and GS departments, as well as the Radiation Protection group: from ...

  5. The Genomic Pattern of tDNA Operon Expression in E. coli.

    Directory of Open Access Journals (Sweden)

    2005-06-01

    Full Text Available In fast-growing microorganisms, a tRNA concentration profile enriched in major isoacceptors selects for the biased usage of cognate codons. This optimizes translational rate for the least mass invested in the translational apparatus. Such translational streamlining is thought to be growth-regulated, but its genetic basis is poorly understood. First, we found in reanalysis of the E. coli tRNA profile that the degree to which it is translationally streamlined is nearly invariant with growth rate. Then, using least squares multiple regression, we partitioned tRNA isoacceptor pools to predicted tDNA operons from the E. coli K12 genome. Co-expression of tDNAs in operons explains the tRNA profile significantly better than tDNA gene dosage alone. Also, operon expression increases significantly with proximity to the origin of replication, oriC, at all growth rates. Genome location explains about 15% of expression variation in a form, at a given growth rate, that is consistent with replication-dependent gene concentration effects. Yet the change in the tRNA profile with growth rate is less than would be expected from such effects. We estimated per-copy expression rates for all tDNA operons that were consistent with independent estimates for rDNA operons. We also found that tDNA operon location, and the location dependence of expression, were significantly different in the leading and lagging strands. The operonic organization and genomic location of tDNA operons are significant factors influencing their expression. Nonrandom patterns of location and strandedness shown by tDNA operons in E. coli suggest that their genomic architecture may be under selection to satisfy physiological demand for tRNA expression at high growth rates.

  6. Accuracy of Genome Reassembly in γ-Irradiated Escherichia coli

    Directory of Open Access Journals (Sweden)

    Jelena Repar

    2013-01-01

    Full Text Available γ-Radiation, a powerful DNA-damaging agent, can often lead to the formation of genome rearrangements. In this study, we have assessed the capacity of Escherichia coli to accurately reassemble its genome after multiple double-strand DNA breaks caused by γ-radiation. It has recently been shown that very high doses of γ-radiation or RecA protein deficiency cause erroneous chromosomal assemblies in Deinococcus radiodurans, a highly radiation-resistant bacterium. Accordingly, we have examined the accuracy of genome reassembly in both wild-type and recA strains of E. coli after exposure to the doses of γ-radiation which reduce the survival by 10^6 - to 10^7 -fold. Thirty-eight percent of wild-type survivors showed gross genome changes, most of which were found to be the consequence of the excision of e14, a 15-kb defective prophage. Only one additional type of gross genome rearrangement was detected, presumably representing the duplication of a DNA fragment. These results demonstrate an unexpectedly accurate genome reassembly in wild-type E. coli. We have detected no genome rearrangements in recA recBCD and recA recBCD sbcB mutants, suggesting that RecA-independent DNA repair in E. coli may also be accurate.

  7. Whole Genome Epidemiological Typing of Escherichia coli

    OpenAIRE

    Kaas, Rolf Sommer; Aarestrup, Frank Møller; Ussery, David; Lund, Ole

    2014-01-01

    Escherichia coli (E. coli) spiller en vigtig rolle i den globale sundhed både grundet dennes rolle som kommensal bakterie, der lever i dennes vært og som patogen bakterie, der er skyld i millioner af infektioner hvert eneste år. Infektionerne er både sporadiske eller som udbrud med tusindvis af smittede i visse tilfælde. For at mindske antallet af infektioner er det vigtigt at overvåge patogene E. coli med henblik på hurtigt opdagelse af udbrud og sporing af kilden til disse. Effektiviteten a...

  8. Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac and Gene Expression in Rust (Uromyces appendiculatus Inoculated Common Bean (Phaseolus vulgaris L..

    Directory of Open Access Journals (Sweden)

    Vasudevan Ayyappan

    Full Text Available Histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. Genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. We report the genome-wide profiling of histone methylation (H3K9me2 and acetylation (H4K12ac in common bean (Phaseolus vulgaris L. under rust (Uromyces appendiculatus stress using two high-throughput approaches, chromatin immunoprecipitation sequencing (ChIP-Seq and RNA sequencing (RNA-Seq. ChIP-Seq analysis revealed 1,235 and 556 histone methylation and acetylation responsive genes from common bean leaves treated with the rust pathogen at 0, 12 and 84 hour-after-inoculation (hai, while RNA-Seq analysis identified 145 and 1,763 genes differentially expressed between mock-inoculated and inoculated plants. The combined ChIP-Seq and RNA-Seq analyses identified some key defense responsive genes (calmodulin, cytochrome p450, chitinase, DNA Pol II, and LRR and transcription factors (WRKY, bZIP, MYB, HSFB3, GRAS, NAC, and NMRA in bean-rust interaction. Differential methylation and acetylation affected a large proportion of stress-responsive genes including resistant (R proteins, detoxifying enzymes, and genes involved in ion flux and cell death. The genes identified were functionally classified using Gene Ontology (GO and EuKaryotic Orthologous Groups (KOGs. The Kyoto Encyclopedia of Genes and Genomes (KEGG pathway analysis identified a putative pathway with ten key genes involved in plant-pathogen interactions. This first report of an integrated analysis of histone modifications and gene expression involved in the bean-rust interaction as reported here provides a comprehensive resource for other epigenomic regulation studies in non-model species under stress.

  9. Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Ayyappan, Vasudevan; Kalavacharla, Venu; Thimmapuram, Jyothi; Bhide, Ketaki P; Sripathi, Venkateswara R; Smolinski, Tomasz G; Manoharan, Muthusamy; Thurston, Yaqoob; Todd, Antonette; Kingham, Bruce

    2015-01-01

    Histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. Genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. We report the genome-wide profiling of histone methylation (H3K9me2) and acetylation (H4K12ac) in common bean (Phaseolus vulgaris L.) under rust (Uromyces appendiculatus) stress using two high-throughput approaches, chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq). ChIP-Seq analysis revealed 1,235 and 556 histone methylation and acetylation responsive genes from common bean leaves treated with the rust pathogen at 0, 12 and 84 hour-after-inoculation (hai), while RNA-Seq analysis identified 145 and 1,763 genes differentially expressed between mock-inoculated and inoculated plants. The combined ChIP-Seq and RNA-Seq analyses identified some key defense responsive genes (calmodulin, cytochrome p450, chitinase, DNA Pol II, and LRR) and transcription factors (WRKY, bZIP, MYB, HSFB3, GRAS, NAC, and NMRA) in bean-rust interaction. Differential methylation and acetylation affected a large proportion of stress-responsive genes including resistant (R) proteins, detoxifying enzymes, and genes involved in ion flux and cell death. The genes identified were functionally classified using Gene Ontology (GO) and EuKaryotic Orthologous Groups (KOGs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified a putative pathway with ten key genes involved in plant-pathogen interactions. This first report of an integrated analysis of histone modifications and gene expression involved in the bean-rust interaction as reported here provides a comprehensive resource for other epigenomic regulation studies in non-model species under stress.

  10. Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods.

    Science.gov (United States)

    Han, Mee-Jung; Yun, Hongseok; Lee, Jeong Wook; Lee, Yu Hyun; Lee, Sang Yup; Yoo, Jong-Shin; Kim, Jin Young; Kim, Jihyun F; Hur, Cheol-Goo

    2011-04-01

    Escherichia coli K-12 and B strains have most widely been employed for scientific studies as well as industrial applications. Recently, the complete genome sequences of two representative descendants of E. coli B strains, REL606 and BL21(DE3), have been determined. Here, we report the subproteome reference maps of E. coli B REL606 by analyzing cytoplasmic, periplasmic, inner and outer membrane, and extracellular proteomes based on the genome information using experimental and computational approaches. Among the total of 3487 spots, 651 proteins including 410 non-redundant proteins were identified and characterized by 2-DE and LC-MS/MS; they include 440 cytoplasmic, 45 periplasmic, 50 inner membrane, 61 outer membrane, and 55 extracellular proteins. In addition, subcellular localizations of all 4205 ORFs of E. coli B were predicted by combined computational prediction methods. The subcellular localizations of 1812 (43.09%) proteins of currently unknown function were newly assigned. The results of computational prediction were also compared with the experimental results, showing that overall precision and recall were 92.16 and 92.16%, respectively. This work represents the most comprehensive analyses of the subproteomes of E. coli B, and will be useful as a reference for proteome profiling studies under various conditions. The complete proteome data are available online (http://ecolib.kaist.ac.kr). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Optics education for K-12

    Science.gov (United States)

    Bilbro, James W.; Gaines Walker, Janice M.

    2000-06-01

    The SPIE Education Committee has developed an outreach program aimed at enhancing the dissemination of information about optics to children in kindergarten through the 12th grade (K-12). The main impetus behind the program was that more practicing optical scientists and engineers would be willing to give lectures and demonstrations aimed at inspiring the next generation about optics if material could be made easily available. Consequently, three instructional `outreach kits' were assembled to use in teaching optics to kids in exciting and fun ways. These kits were beta-tested over the last two years at six different U.S. regional sites. Each `outreach kit' contained: (1) a workbook on Optical Demonstrations on the Overhead Projector; (2) a Science and Math Experience Manual: Light, Color and Their Uses; (3) The Optics Discovery Classroom Kit; (4) a slide show; and (5) a video on careers in optics. The best tests were aimed at evaluating the practical ways of utilizing the kits, developing easy-to-follow instructions for guiding others in their use and providing suggestions on modifications, additions, and deletions to the kits. This paper discuses this outreach program and provides details relative to the kit's composition and future plans.

  12. Genome-scale genetic engineering in Escherichia coli.

    Science.gov (United States)

    Jeong, Jaehwan; Cho, Namjin; Jung, Daehee; Bang, Duhee

    2013-11-01

    Genome engineering has been developed to create useful strains for biological studies and industrial uses. However, a continuous challenge remained in the field: technical limitations in high-throughput screening and precise manipulation of strains. Today, technical improvements have made genome engineering more rapid and efficient. This review introduces recent advances in genome engineering technologies applied to Escherichia coli as well as multiplex automated genome engineering (MAGE), a recent technique proposed as a powerful toolkit due to its straightforward process, rapid experimental procedures, and highly efficient properties. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Author Reply to K12 Inc. Response

    Science.gov (United States)

    National Education Policy Center, 2012

    2012-01-01

    K12 Inc. enrolls more public school students than any other private education management organization in the U.S. Much has been written about K12 Inc. (referred to in this report simply as "K12") by financial analysts and investigative journalists because it is a large, publicly traded company and is the dominant player in the operation…

  14. Comparison of 61 Sequenced Escherichia coli Genomes

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Wassenaar, T. M.; Ussery, David

    2010-01-01

    trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico...... MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or 'accessory' genes thus make up more than 90...

  15. Multiplex Genome Editing in Escherichia coli

    DEFF Research Database (Denmark)

    Ingemann Jensen, Sheila; Nielsen, Alex Toftgaard

    2018-01-01

    Lambda Red recombineering is an easy and efficient method for generating genetic modifications in Escherichia coli. For gene deletions, lambda Red recombineering is combined with the use of selectable markers, which are removed through the action of, e.g., flippase (Flp) recombinase. This PCR...

  16. Comparative Genomics of Escherichia coli Strains Causing Urinary Tract Infections

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk; Hancock, Viktoria; Schembri, Mark A.

    2011-01-01

    The virulence determinants of uropathogenic Escherichia coli have been studied extensively over the years, but relatively little is known about what differentiates isolates causing various types of urinary tract infections. In this study, we compared the genomic profiles of 45 strains from a range...... of different clinical backgrounds, i.e., urosepsis, pyelonephritis, cystitis, and asymptomatic bacteriuria (ABU), using comparative genomic hybridization analysis. A microarray based on 31 complete E. coli sequences was used. It emerged that there is little correlation between the genotypes of the strains...... disease categories were identified. Among these were two genomic islands, namely, pathogenicity island (PAI)-CFT073-serU and PAI-CFT073-pheU, which were significantly more associated with the pyelonephritis and urosepsis isolates than with the ABU and cystitis isolates. These two islands harbor genes...

  17. Genome Sequence and Analysis of Escherichia coli MRE600, a Colicinogenic, Nonmotile Strain that Lacks RNase I and the Type I Methyltransferase, EcoKI.

    Science.gov (United States)

    Kurylo, Chad M; Alexander, Noah; Dass, Randall A; Parks, Matthew M; Altman, Roger A; Vincent, C Theresa; Mason, Christopher E; Blanchard, Scott C

    2016-01-22

    Escherichia coli strain MRE600 was originally identified for its low RNase I activity and has therefore been widely adopted by the biomedical research community as a preferred source for the expression and purification of transfer RNAs and ribosomes. Despite its widespread use, surprisingly little information about its genome or genetic content exists. Here, we present the first de novo assembly and description of the MRE600 genome and epigenome. To provide context to these studies of MRE600, we include comparative analyses with E. coli K-12 MG1655 (K12). Pacific Biosciences Single Molecule, Real-Time sequencing reads were assembled into one large chromosome (4.83 Mb) and three smaller plasmids (89.1, 56.9, and 7.1 kb). Interestingly, the 7.1-kb plasmid possesses genes encoding a colicin E1 protein and its associated immunity protein. The MRE600 genome has a G + C content of 50.8% and contains a total of 5,181 genes, including 4,913 protein-encoding genes and 268 RNA genes. We identified 41,469 modified DNA bases (0.83% of total) and found that MRE600 lacks the gene for type I methyltransferase, EcoKI. Phylogenetic, taxonomic, and genetic analyses demonstrate that MRE600 is a divergent E. coli strain that displays features of the closely related genus, Shigella. Nevertheless, comparative analyses between MRE600 and E. coli K12 show that these two strains exhibit nearly identical ribosomal proteins, ribosomal RNAs, and highly homologous tRNA species. Substantiating prior suggestions that MRE600 lacks RNase I activity, the RNase I-encoding gene, rna, contains a single premature stop codon early in its open-reading frame. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Two Tales of Prokaryotic Genomic Diversity: Escherichia coli and Halophiles

    Directory of Open Access Journals (Sweden)

    Lejla Pašić

    2014-01-01

    Full Text Available Prokaryotes are generally characterized by vast genomic diversity that has been shaped by mutations, horizontal gene transfer, bacteriocins and phage predation. Enormous genetic diversity has developed as a result of stresses imposed in harsh environments and the ability of microorganisms to adapt. Two examples of prokaryotic diversity are presented: on intraspecies level, exemplified by Escherichia coli, and the diversity of the hypersaline environment, with the discussion of food-related health issues and biotechnological potential.

  19. Role of bolA and rpoS genes in biofilm formation and adherence pattern by Escherichia coli K-12 MG1655 on polypropylene, stainless steel, and silicone surfaces.

    Science.gov (United States)

    Adnan, Mohd; Sousa, Ana Margarida; Machado, Idalina; Pereira, Maria Olivia; Khan, Saif; Morton, Glyn; Hadi, Sibte

    2017-06-01

    Escherichia coli has developed sophisticated means to sense, respond, and adapt in stressed environment. It has served as a model organism for studies in molecular genetics and physiology since the 1960s. Stress response genes are induced whenever a cell needs to adapt and survive under unfavorable growth conditions. Two of the possible important genes are rpoS and bolA. The rpoS gene has been known as the alternative sigma (σ) factor, which controls the expression of a large number of genes, which are involved in responses to various stress factors as well as transition to stationary phase from exponential form of growth. Morphogene bolA response to stressed environment leads to round morphology of E. coli cells, but little is known about its involvement in biofilms and its development or maintenance. This study has been undertaken to address the adherence pattern and formation of biofilms by E. coli on stainless steel, polypropylene, and silicone surfaces after 24 h of growth at 37 °C. Scanning electron microscopy was used for direct examination of the cell attachment and biofilm formation on various surfaces and it was found that, in the presence of bolA, E. coli cells were able to attach to the stainless steel and silicone very well. By contrast, polypropylene surface was not found to be attractive for E. coli cells. This indicates that bolA responded and can play a major role in the presence and absence of rpoS in cell attachment.

  20. Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitro support the role of conjugation for horizontal transfer of genomic islands

    Directory of Open Access Journals (Sweden)

    Hochhut Bianca

    2011-09-01

    Full Text Available Abstract Background A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs - including pathogenicity islands (PAIs - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT. Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K, an origin of transfer (oriTRP4 and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536. Conclusions Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.

  1. Three clustered origins of replication in a promiscuous-plasmid replicon and their differential use in a PolA+ strain and a delta PolA strain of Escherichia coli K-12.

    OpenAIRE

    Banerjee, S. K.; Luck, B T; Kim, H Y; Iyer, V. N.

    1992-01-01

    A 1,197-bp region of the broad-host-range plasmid pCU1 is adequate for its replication. Analysis of replicating molecules containing this region reveals three clustered origins of vegetative replication and replication proceeds bidirectionally from each in a theta mode. In an Escherichia coli polymerase I deletion mutant, utilization of one of these three origins was not detected. The potentiality for origin utilization may therefore be a determinant of replicon host range.

  2. Three clustered origins of replication in a promiscuous-plasmid replicon and their differential use in a PolA+ strain and a delta PolA strain of Escherichia coli K-12.

    Science.gov (United States)

    Banerjee, S K; Luck, B T; Kim, H Y; Iyer, V N

    1992-12-01

    A 1,197-bp region of the broad-host-range plasmid pCU1 is adequate for its replication. Analysis of replicating molecules containing this region reveals three clustered origins of vegetative replication and replication proceeds bidirectionally from each in a theta mode. In an Escherichia coli polymerase I deletion mutant, utilization of one of these three origins was not detected. The potentiality for origin utilization may therefore be a determinant of replicon host range.

  3. Recombinational construction in Escherichia coli of infectious adenoviral genomes

    Science.gov (United States)

    Crouzet, Joël; Naudin, Laurent; Orsini, Cécile; Vigne, Emmanuelle; Ferrero, Lucy; Le Roux, Aude; Benoit, Patrick; Latta, Martine; Torrent, Christophe; Branellec, Didier; Denèfle, Patrice; Mayaux, Jean-François; Perricaudet, Michel; Yeh, Patrice

    1997-01-01

    A two-step gene replacement procedure was developed that generates infectious adenoviral genomes through homologous recombination in Escherichia coli. As a prerequisite, a human adenovirus serotype 5 (Ad5)-derived genome was first introduced as a PacI restriction fragment into an incP-derived replicon which, in contrast to ColE1-derivatives (e.g., pBR322 or pUC plasmids), is functional in a polA mutant of E. coli. Any modification can be introduced at will following two consecutive homologous recombinations between the incP/Ad5 replicon and the ColE1 plasmid. The overall procedure requires only the in vitro engineering of the ColE1-derivative by flanking the desired modification with small stretches of identical sequences. In the first step, a cointegrate between the tetracycline-resistant incP/Ad5 replicon and the kanamycin-resistant ColE1-derivative is selected by growing the polA host in the presence of both antibiotics. Resolution of this cointegrate is further selected in sucrose growth conditions due to the loss of a conditional suicide marker (the sacB gene of Bacillus subtilis) present in the ColE1 plasmid, leading to unmodified and modified incP/Ad5 replicons that can be differentiated upon restriction analysis. Consecutive rounds of this two-step cloning procedure allowed the introduction of multiple independent modifications within the virus genome, with no requirement for an intermediate virus. The potential of this procedure is demonstrated by the recovery of several E1E3E4-deleted adenoviruses following transfection of the corresponding E. coli-derived genomes in IGRP2 cells. PMID:9037067

  4. K-12 Educational Outcomes of Immigrant Youth

    National Research Council Canada - National Science Library

    Robert Crosnoe; Ruth N. López Turley

    2011-01-01

    The children from immigrant families in the United States make up a historically diverse population, and they are demonstrating just as much diversity in their experiences in the K-12 educational system...

  5. Nebraska Science Standards: Grades K-12

    Science.gov (United States)

    Nebraska Department of Education, 2010

    2010-01-01

    This publication presents the Nebraska Science Standards for Grades K-12. The standards are presented according to the following grades: (1) Grades K-2; (2) Grades 3-5; (3) Grades 6-8; and (4) Grades 9-12.

  6. Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Vincent P Richards

    Full Text Available Escherichia coli is an important cause of bovine mastitis and can cause both severe inflammation with a short-term transient infection, as well as less severe, but more chronic inflammation and infection persistence. E. coli is a highly diverse organism that has been classified into a number of different pathotypes or pathovars, and mammary pathogenic E. coli (MPEC has been proposed as a new such pathotype. The purpose of this study was to use genome sequence data derived from both transient and persistent MPEC isolates (two isolates of each phenotype to construct a genome-based phylogeny that places MPEC in its phylogenetic context with other E. coli pathovars. A subsidiary goal was to conduct comparative genomic analyses of these MPEC isolates with other E. coli pathovars to provide a preliminary perspective on loci that might be correlated with the MPEC phenotype. Both concatenated and consensus tree phylogenies did not support MPEC monophyly or the monophyly of either transient or persistent phenotypes. Three of the MPEC isolates (ECA-727, ECC-Z, and ECA-O157 originated from within the predominately commensal clade of E. coli, referred to as phylogroup A. The fourth MPEC isolate, of the persistent phenotype (ECC-1470, was sister group to an isolate of ETEC, falling within the E. coli B1 clade. This suggests that the MPEC phenotype has arisen on numerous independent occasions and that this has often, although not invariably, occurred from commensal ancestry. Examination of the genes present in the MPEC strains relative to the commensal strains identified a consistent presence of the type VI secretion system (T6SS in the MPEC strains, with only occasional representation in commensal strains, suggesting that T6SS may be associated with MPEC pathogenesis and/or as an inter-bacterial competitive attribute and therefore could represent a useful target to explore for the development of MPEC specific inhibitors.

  7. A series of template plasmids for Escherichia coli genome engineering.

    Science.gov (United States)

    Deb, Shalini S; Reshamwala, Shamlan M S; Lali, Arvind M

    2016-06-01

    Metabolic engineering strategies often employ multi-copy episomal vectors to overexpress genes. However, chromosome-based overexpression is preferred as it avoids the use of selective pressure and reduces metabolic burden on the cell. We have constructed a series of template plasmids for λ Red-mediated Escherichia coli genome engineering. The template plasmids allow construction of genome integrating cassettes that can be used to integrate single copies of DNA sequences at predetermined sites or replace promoter regions. The constructed cassettes provide flexibility in terms of expression levels achieved and antibiotics used for selection, as well as allowing construction of marker-free strains. The modular design of the template plasmids allows replacement of genetic parts to construct new templates. Gene integration and promoter replacement using the template plasmids are illustrated. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth.

    Directory of Open Access Journals (Sweden)

    Alessandro G Franchini

    Full Text Available For heterotrophic microbes, limited availability of carbon and energy sources is one of the major nutritional factors restricting the rate of growth in most ecosystems. Physiological adaptation to this hunger state requires metabolic versatility which usually involves expression of a wide range of different catabolic pathways and of high-affinity carbon transporters; together, this allows for simultaneous utilization of mixtures of carbonaceous compounds at low concentrations. In Escherichia coli the stationary phase sigma factor RpoS and the signal molecule cAMP are the major players in the regulation of transcription under such conditions; however, their interaction is still not fully understood. Therefore, during growth of E. coli in carbon-limited chemostat culture at different dilution rates, the transcriptomes, expression of periplasmic proteins and catabolomes of strains lacking one of these global regulators, either rpoS or adenylate cyclase (cya, were compared to those of the wild-type strain. The inability to synthesize cAMP exerted a strong negative influence on the expression of alternative carbon source uptake and degradation systems. In contrast, absence of RpoS increased the transcription of genes belonging to high-affinity uptake systems and central metabolism, presumably due to reduced competition of σ(D with σ(S. Phenotypical analysis confirmed this observation: The ability to respire alternative carbon substrates and to express periplasmic high-affinity binding proteins was eliminated in cya and crp mutants, while these properties were not affected in the rpoS mutant. As expected, transcription of numerous stress defence genes was negatively affected by the rpoS knock-out mutation. Interestingly, several genes of the RpoS stress response regulon were also down-regulated in the cAMP-negative strain indicating a coordinated global regulation. The results demonstrate that cAMP is crucial for catabolic flexibility during slow

  9. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence

    Directory of Open Access Journals (Sweden)

    Karmali Mohamed A

    2009-06-01

    Full Text Available Abstract Background Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH. Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP typing. In this study an in silico comparison of six different genotyping approaches was performed on 19 E. coli genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7 strains. Results In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E. coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains. Conclusion The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping

  10. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Hallin, Peter Fischer; Wassenaar, Trudy

    2007-01-01

    of the same species are rapidly becoming available, allowing for the definition and characterization of a whole species as a population of genomes - the 'pan-genome'. Results: Using 32 Escherichia coli and Shigella genome sequences we estimate the pan- and core genome of the species. We designed a high...

  11. Development of K-12 Engineering Outreach Materials

    Science.gov (United States)

    Jordan, William

    2003-01-01

    Six modules were created that can be used in K-12 classes to introduce students to what engineers can do at NASA.The purpose of this project was to create outreach materials for the classroom. To make it appealing to students, many color NASA photographs are used to illustrate NASA applications.Student experiments are described that can be performed to illustrate topics.

  12. Copyright Updates for K-12 Librarians

    Science.gov (United States)

    Johnson, Wendell G.

    2016-01-01

    Copyright concerns continue to bedevil K-12 librarians, who are often called upon to act as the copyright officers in public schools. This article describes recent copyright developments of concern to these librarians in three areas: a recent court case involving a university library, pending legislation supported by ALA, and a regulatory update.…

  13. Physical Education Curriculum Framework K-12.

    Science.gov (United States)

    Tennessee State Dept. of Education, Nashville.

    This monograph presents a framework for physical education programs in Tennessee for grades K-12. The framework covers four areas: (1) games/sports; (2) gymnastics; (3) physical fitness; and (4) rhythmic movement. The goals and objectives for each of these areas are outlined and described for all grade levels. (JD)

  14. Approaching K-12 Online Education in Pennsylvania

    Science.gov (United States)

    Vadell, Kathryn

    2013-01-01

    The purpose of this study is to determine how K-12 schools are addressing the need to accommodate online learners in Pennsylvania. It is built upon a review of literature focusing on educational legislation, the personalization of online learning and online learning solutions. The study posed 21 questions utilizing a mixed methods approach to…

  15. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

    DEFF Research Database (Denmark)

    Kaas, Rolf Sommer; Rundsten, Carsten Friis; Ussery, David

    2012-01-01

    for creating better phylogenies, for determination of molecular clocks and for improved typing techniques. Results We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former 'soft core' of about 3,000 gene families is perhaps...... more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters. A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence, maps the relatedness...... of the 186 sequenced E. coli genomes. The core-gene tree displays high confidence and divides the E. coli strains into the observed MLST type clades and also separates defined phylotypes. Conclusion The results of comparing a large and diverse E. coli dataset support the theory that reliable and good...

  16. Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli.

    Science.gov (United States)

    Hazen, Tracy H; Michalski, Jane; Luo, Qingwei; Shetty, Amol C; Daugherty, Sean C; Fleckenstein, James M; Rasko, David A

    2017-06-14

    Escherichia coli that are capable of causing human disease are often classified into pathogenic variants (pathovars) based on their virulence gene content. However, disease-associated hybrid E. coli, containing unique combinations of multiple canonical virulence factors have also been described. Such was the case of the E. coli O104:H4 outbreak in 2011, which caused significant morbidity and mortality. Among the pathovars of diarrheagenic E. coli that cause significant human disease are the enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC). In the current study we use comparative genomics, transcriptomics, and functional studies to characterize isolates that contain virulence factors of both EPEC and ETEC. Based on phylogenomic analysis, these hybrid isolates are more genomically-related to EPEC, but appear to have acquired ETEC virulence genes. Global transcriptional analysis using RNA sequencing, demonstrated that the EPEC and ETEC virulence genes of these hybrid isolates were differentially-expressed under virulence-inducing laboratory conditions, similar to reference isolates. Immunoblot assays further verified that the virulence gene products were produced and that the T3SS effector EspB of EPEC, and heat-labile toxin of ETEC were secreted. These findings document the existence and virulence potential of an E. coli pathovar hybrid that blurs the distinction between E. coli pathovars.

  17. Genome-wide transcriptome analysis of fluoroquinolone resistance in clinical isolates of Escherichia coli.

    Science.gov (United States)

    Yamane, Takashi; Enokida, Hideki; Hayami, Hiroshi; Kawahara, Motoshi; Nakagawa, Masayuki

    2012-04-01

    Coincident with their worldwide use, resistance to fluoroquinolones in Escherichia coli has increased. To identify the gene expression profiles underlying fluoroquinolone resistance, we carried out genome-wide transcriptome analysis of fluoroquinolone-sensitive E. coli. Four fluoroquinolone-sensitive E. coli and five fluoroquinolone-resistant E. coli clinical isolates were subjected to complementary deoxyribonucleic acid microarray analysis. Some upregulated genes' expression was verified by real-time polymerase chain reaction using 104 E. coli clinical isolates, and minimum inhibitory concentration tests were carried out by using their transformants. A total of 40 genes were significantly upregulated in fluoroquinolone-resistant E. coli isolates (P operons, which are involved in biofilm formation, was markedly upregulated in our profile of fluoroquinolone-resistant E. coli. One of the phage shock protein operons, pspC, was significantly upregulated in 50 fluoroquinolone-resistant E. coli isolates (P operons involved in biofilm formation, were markedly downregulated in fluoroquinolone-resistant E. coli. Deoxyribonucleic acid adenine methyltransferase (dam), which represses type I fimbriae genes, was significantly upregulated in the clinical fluoroquinolone-resistant E. coli isolates (P = 0.007). We established pspC- and dam-expressing E. coli transformants from fluoroquinolone-sensitive E. coli, and the minimum inhibitory concentration tests showed that the transformants acquired fluoroquinolone resistance, suggesting that upregulation of these genes contributes to acquiring fluoroquinolone resistance. Upregulation of psp operones and dam underlying pilus operons downregulation might be associated with fluoroquinolone resistance in E. coli. © 2011 The Japanese Urological Association.

  18. Comparative genomics of European avian pathogenic E. Coli (APEC).

    Science.gov (United States)

    Cordoni, Guido; Woodward, Martin J; Wu, Huihai; Alanazi, Mishaal; Wallis, Tim; La Ragione, Roberto M

    2016-11-22

    Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were characterised using multiplex polymerase chain reactions (PCRs) targeting 22 equally weighted factors covering virulence genes, R-type and phylogroup. Following these analysis, 95 of the selected strains were further analysed using Whole Genome Sequencing (WGS). The most prevalent phylogroups were B2 (47%) and A1 (22%), although there were national differences with Germany presenting group B2 (35.3%), Italy presenting group A1 (53.3%) and UK presenting group B2 (56.1%) as the most prevalent. R-type R1 was the most frequent type (55%) among APEC, but multiple R-types were also frequent (26.8%). Following compilation of all the PCR data which covered a total of 15 virulence genes, it was possible to build a similarity tree using each PCR result unweighted to produce 9 distinct groups. The average number of virulence genes was 6-8 per isolate, but no positive association was found between phylogroup and number or type of virulence genes. A total of 95 isolates representing each of these 9 groupings were genome sequenced and analysed for in silico serotype, Multilocus Sequence Typing (MLST), and antimicrobial resistance (AMR). The UK isolates showed the greatest variability in terms of serotype and MLST compared with German and Italian isolates, whereas the lowest prevalence of AMR was found for German isolates. Similarity trees were compiled using sequencing data and notably single nucleotide polymorphism data generated ten distinct geno-groups. The frequency of geno-groups across Europe comprised 26.3% belonging to Group 8 representing serogroups O2, O4, O18 and MLST types ST95, ST140, ST141, ST428, ST1618 and others, 18.9% belonging to Group 1 (serogroups O78 and

  19. Complete genome sequence of the avian pathogenic Escherichia coli strain APEC O78.

    Science.gov (United States)

    Mangiamele, Paul; Nicholson, Bryon; Wannemuehler, Yvonne; Seemann, Torsten; Logue, Catherine M; Li, Ganwu; Tivendale, Kelly A; Nolan, Lisa K

    2013-03-21

    Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is a significant disease, causing extensive animal and financial losses globally. Because of the significance of this disease, more knowledge is needed regarding APEC's mechanisms of virulence. Here, we present the fully closed genome sequence of a typical avian pathogenic E. coli strain belonging to the serogroup O78.

  20. Isolation and genomic characterization of Escherichia coli O157:NM ...

    African Journals Online (AJOL)

    Human diseases caused by Escherichia coli O157:NM and E. coli O157:H7 strains have been reported throughout the world. In developed countries, serotype O157:H7 represents the major cause of human diseases; however, there have been increasing reports of non-O157 Shiga toxin (Stx)-producing E. coli strains ...

  1. A draft genome of Escherichia coli sequence type 127 strain 2009-46.

    Science.gov (United States)

    Darling, Aaron E; McKinnon, Jessica; Worden, Paul; Santos, Jerran; Charles, Ian G; Chowdhury, Piklu Roy; Djordjevic, Steven P

    2014-01-01

    Escherichia coli are a frequent cause of urinary tract infections (UTI) and are thought to have a foodborne origin. E. coli with sequence type 127 (ST127) are emerging pathogens increasingly implicated as a cause of urinary tract infections (UTI) globally. A ST127 isolate (2009-46) resistant to ampicillin and trimethoprim was recovered from the urine of a 56 year old patient with a UTI from a hospital in Sydney, Australia and was characterised here. We sequenced the genome of Escherichia coli 2009-46 using the Illumina Nextera XT and MiSeq technologies. Assembly of the sequence data reconstructed a 5.14 Mbp genome in 89 scaffolds with an N50 of 161 kbp. The genome has extensive similarity to other sequenced uropathogenic E. coli genomes, but also has several genes that are potentially related to virulence and pathogenicity that are not present in the reference E. coli strain. E. coli 2009-46 is a multiple antibiotic resistant, phylogroup B2 isolate recovered from a patient with a UTI. This is the first description of a drug resistant E. coli ST127 in Australia.

  2. A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase•tRNAHispair.

    Science.gov (United States)

    Englert, Markus; Vargas-Rodriguez, Oscar; Reynolds, Noah M; Wang, Yane-Shih; Söll, Dieter; Umehara, Takuya

    2017-11-01

    Development of new aminoacyl-tRNA synthetase (aaRS)•tRNA pairs is central for incorporation of novel non-canonical amino acids (ncAAs) into proteins via genetic code expansion (GCE). The Escherichia coli and Caulobacter crescentus histidyl-tRNA synthetases (HisRS) evolved divergent mechanisms of tRNA His recognition that prevent their cross-reactivity. Although the E. coli HisRS•tRNA His pair is a good candidate for GCE, its use in C. crescentus is limited by the lack of established genetic selection methods and by the low transformation efficiency of C. crescentus. E. coli was genetically engineered to use a C. crescentus HisRS•tRNA His pair. Super-folder green fluorescent protein (sfGFP) and chloramphenicol acetyltransferase (CAT) were used as reporters for read-through assays. A library of 313 ncAAs coupled with the sfGFP reporter system was employed to investigate the specificity of E. coli HisRS in vivo. A genomically modified E. coli strain (named MEOV1) was created. MEVO1 requires an active C. crescentus HisRS•tRNA His pair for growth, and displays a similar doubling time as the parental E. coli strain. sfGFP- and CAT-based assays showed that the E. coli HisRS•tRNA His pair is orthogonal in MEOV1 cells. A mutation in the anticodon loop of E. coli tRNA His CUA elevated its suppression efficiency by 2-fold. The C. crescentus HisRS•tRNA His pair functionally complements an E. coli ΔhisS strain. The E. coli HisRS•tRNA His is orthogonal in MEOV1 cells. E. coli tRNA His CUA is an efficient amber suppressor in MEOV1. We developed a platform that allows protein engineering of E. coli HisRS that should facilitate GCE in E. coli. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

    Science.gov (United States)

    Robins-Browne, Roy M; Holt, Kathryn E; Ingle, Danielle J; Hocking, Dianna M; Yang, Ji; Tauschek, Marija

    2016-01-01

    The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods.

  4. Comparative genomics of Escherichia coli isolated from patients with inflammatory bowel disease

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk; Hancock, Viktoria; Petersen, Andreas M.

    2011-01-01

    both host-genetic and exogenous factors have been found to be involved, the aetiology of IBD is still not well understood. In this study we characterized thirteen Escherichia coli strains from patients with IBD by comparative genomic hybridization employing a microarray based on 31 sequenced E. coli...... with the prototypic CD isolate, LF82, suggesting that the IBD-inducing effect of the strains is multifactorial. Several of the IBD isolates carried a number of extraintestinal pathogenic E. coli (ExPEC)-related virulence determinants such as the pap, sfa, cdt and hly genes. The isolates were also found to carry genes...... of ExPEC-associated genomic islands. Conclusions: Combined, these data suggest that E. coli isolates obtained from UC and CD patients represents a heterogeneous population of strains, with genomic profiles that are indistinguishable to those of ExPEC isolates. Our findings indicate that IBD...

  5. K-12 educational outcomes of immigrant youth.

    Science.gov (United States)

    Crosnoe, Robert; Turley, Ruth N López

    2011-01-01

    The children from immigrant families in the United States make up a historically diverse population, and they are demonstrating just as much diversity in their experiences in the K-12 educational system. Robert Crosnoe and Ruth López Turley summarize these K-12 patterns, paying special attention to differences in academic functioning across segments of the immigrant population defined by generational status, race and ethnicity, and national origin. A good deal of evidence points to an immigrant advantage in multiple indicators of academic progress, meaning that many youths from immigrant families outperform their peers in school. This apparent advantage is often referred to as the immigrant paradox, in that it occurs despite higher-than-average rates of social and economic disadvantages in this population as a whole. The immigrant paradox, however, is more pronounced among the children of Asian and African immigrants than other groups, and it is stronger for boys than for girls. Furthermore, evidence for the paradox is far more consistent in secondary school than in elementary school. Indeed, school readiness appears to be one area of potential risk for children from immigrant families, especially those of Mexican origin. For many groups, including those from Latin America, any evidence of the immigrant paradox usually emerges after researchers control for family socioeconomic circumstances and youths' English language skills. For others, including those from Asian countries, it is at least partially explained by the tendency for more socioeconomically advantaged residents of those regions to leave their home country for the United States. Bilingualism and strong family ties help to explain immigrant advantages in schooling; school, community, and other contextual disadvantages may suppress these advantages or lead to immigrant risks. Crosnoe and Turley also discuss several policy efforts targeting young people from immigrant families, especially those of Latin

  6. K-12 Teaching and Physics Enrollment

    CERN Document Server

    Masood, Samina S

    2014-01-01

    We have collected and analyzed the relevant data from public schools in greater Houston area of Texas. Based and analyzed. Since the data is only limited to a few school, we are still working on getting more data so that we can compare and contrast the results adequately and understand the core of the enrollment issue at the national level. However, based on the raw data and partial analysis, we propose a few recommendations towards the improvement of science education in Texas Schools, in general, and greater Houston area schools in particular. Our results indicate that the quality of science education can be improved significantly if we focus on the improvement of high school education or even intermediate schools when students are first time exposed to science in a little technical way. Simply organizing teacher training programs at K-12 level as school education plays a pivotal role in the decrease in physics enrollment at the higher level. Similar analysis can actually be generalized to other states to f...

  7. Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics.

    Science.gov (United States)

    Hazen, Tracy H; Leonard, Susan R; Lampel, Keith A; Lacher, David W; Maurelli, Anthony T; Rasko, David A

    2016-08-01

    Enteroinvasive Escherichia coli (EIEC) is a unique pathovar that has a pathogenic mechanism nearly indistinguishable from that of Shigella species. In contrast to isolates of the four Shigella species, which are widespread and can be frequent causes of human illness, EIEC causes far fewer reported illnesses each year. In this study, we analyzed the genome sequences of 20 EIEC isolates, including 14 first described in this study. Phylogenomic analysis of the EIEC genomes demonstrated that 17 of the isolates are present in three distinct lineages that contained only EIEC genomes, compared to reference genomes from each of the E. coli pathovars and Shigella species. Comparative genomic analysis identified genes that were unique to each of the three identified EIEC lineages. While many of the EIEC lineage-specific genes have unknown functions, those with predicted functions included a colicin and putative proteins involved in transcriptional regulation or carbohydrate metabolism. In silico detection of the Shigella virulence plasmid (pINV), which is essential for the invasion of host cells, demonstrated that a form of pINV was present in nearly all EIEC genomes, but the Mxi-Spa-Ipa region of the plasmid that encodes the invasion-associated proteins was absent from several of the EIEC isolates. The comparative genomic findings in this study support the hypothesis that multiple EIEC lineages have evolved independently from multiple distinct lineages of E. coli via the acquisition of the Shigella virulence plasmid and, in some cases, the Shigella pathogenicity islands. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  8. A simple and effective method for construction of Escherichia coli strains proficient for genome engineering.

    Science.gov (United States)

    Ryu, Young Shin; Biswas, Rajesh Kumar; Shin, Kwangsu; Parisutham, Vinuselvi; Kim, Suk Min; Lee, Sung Kuk

    2014-01-01

    Multiplex genome engineering is a standalone recombineering tool for large-scale programming and accelerated evolution of cells. However, this advanced genome engineering technique has been limited to use in selected bacterial strains. We developed a simple and effective strain-independent method for effective genome engineering in Escherichia coli. The method involves introducing a suicide plasmid carrying the λ Red recombination system into the mutS gene. The suicide plasmid can be excised from the chromosome via selection in the absence of antibiotics, thus allowing transient inactivation of the mismatch repair system during genome engineering. In addition, we developed another suicide plasmid that enables integration of large DNA fragments into the lacZ genomic locus. These features enable this system to be applied in the exploitation of the benefits of genome engineering in synthetic biology, as well as the metabolic engineering of different strains of E. coli.

  9. Colorado K-12 & School Choice Survey: What Do Voters Say about K-12 Education? Polling Paper No. 26

    Science.gov (United States)

    DiPerna, Paul

    2015-01-01

    The purpose of the "Colorado K-12 & School Choice Survey" is to measure public opinion on, and in some cases awareness or knowledge of, a range of K-12 education topics and school choice reforms. A total of 601 telephone interviews were completed from August 29 to September 16, 2015, with questions on the direction of K-12 education,…

  10. A draft genome of Escherichia coli sequence type 127 strain 2009-46

    OpenAIRE

    Darling, Aaron E; McKinnon, Jessica; Worden, Paul; Santos, Jerran; Charles, Ian G; Chowdhury, Piklu Roy; Djordjevic, Steven P

    2014-01-01

    Background Escherichia coli are a frequent cause of urinary tract infections (UTI) and are thought to have a foodborne origin. E. coli with sequence type 127 (ST127) are emerging pathogens increasingly implicated as a cause of urinary tract infections (UTI) globally. A ST127 isolate (2009-46) resistant to ampicillin and trimethoprim was recovered from the urine of a 56 year old patient with a UTI from a hospital in Sydney, Australia and was characterised here. Results We sequenced the genome ...

  11. Complete Genome Sequence of the Escherichia coli PMV-1 Strain, a Model Extraintestinal Pathogenic E. coli Strain Used for Host-Pathogen Interaction Studies

    OpenAIRE

    Peris-Bondia, Francesc; Muraille, Eric; Van Melderen, Laurence

    2013-01-01

    Escherichia coli is a highly versatile species, causing diverse intestinal and extraintestinal infections. Here, we present the complete genome sequence of PMV-1, an O18:K1 extraintestinal pathogenic E.?coli (ExPEC) strain that is used as a model for peritonitis in mice and was useful for deciphering the innate immune response triggered by ExPEC infections.

  12. PCR-based tandem epitope tagging system for Escherichia coli genome engineering.

    Science.gov (United States)

    Cho, Byung-Kwan; Knight, Eric M; Palsson, Bernhard O

    2006-01-01

    Biological discovery in the postgenomic era requires a systematic and high-throughput experimental approach. To this end, a versatile PCR-based tandem epitope tagging system is described, which inserts a tandem epitope coding sequence into any desired position of the Escherichia coli chromosome. Template plasmids were constructed that carry tandem copies of the epitope encoding sequence, Flp recombinase target (FRT) sites, and antibiotic resistance genes. The linear DNA fragment, amplified from the template plasmid with extensions homologous to the end of the target gene and part of its downstream region, was transformed into E. coli K-12 MG1655 harboring the bacteriophage gamma Red recombination system. The antibiotic resistance gene was then removed from the inserted heterologous PCR fragment using Flp recombinase. This epitope tagging system was applied to global transcription factors of E. coli to obtain proteins fused with tandem c-myc epitope tags. The tandem myc epitope-fused transcription factors were successfully detected by Western blot analysis and chromatin immunoprecipitation with increased detection sensitivity and higher yield. Higher copy numbers of the epitope molecule allowed the use of more stringent experimental conditions to increase the signal-to-noise ratio in subsequent experimental applications. Furthermore, judging from the measurement of gene expression using reverse transcription PCR (RT-PCR), the epitope-fused transcription factors retained their normal function for gene regulation in vivo.

  13. High incidence of multiple antibiotic resistant cells in cultures of in enterohemorrhagic Escherichia coli O157:H7

    OpenAIRE

    Carone, Benjamin R.; Xu, Tao; Murphy, Kenan C.; Marinus, Martin G.

    2013-01-01

    The spontaneous incidence of chloramphenicol (Cam) resistant mutant bacteria is at least ten-fold higher in cultures of enterohemorrhagic E. coli O157:H7 strain EDL933 than in E. coli K-12. It is at least 100-fold higher in the dam (DNA adenine methyltransferase) derivative of EDL933, compared to the dam strain of E. coli K-12, thereby preventing the use of Cam resistance as a marker in gene replacement technology. Genome sequencing of Cam-resistant isolates of EDL933 and its dam derivatives ...

  14. Complete Genome Sequence of the Avian-Pathogenic Escherichia coli Strain APEC O18.

    Science.gov (United States)

    Nicholson, Bryon A; Wannemuehler, Yvonne M; Logue, Catherine M; Li, Ganwu; Nolan, Lisa K

    2016-11-03

    Avian-pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, a disease that affects all facets of poultry production worldwide, resulting in multimillion dollar losses annually. Here, we report the genome sequence of an APEC O18 sequence type 95 (ST95) strain associated with disease in a chicken. Copyright © 2016 Nicholson et al.

  15. Whole-genome sequence of Escherichia coli serotype O157:H7 strain B6914-ARS

    Science.gov (United States)

    Escherichia coli serotype O157:H7 strain B6914-MS1 is a Shiga toxin-deficient human fecal isolate obtained by the Centers for Disease Control and Prevention that has been used extensively in applied research studies. Here we report the genome sequence of strain B6914-ARS, a B6914-MS1 clone that has ...

  16. Characterization of C. jejuni and C. coli broiler isolates by whole genome sequencing

    DEFF Research Database (Denmark)

    Cantero, G.; Correa-Fiz, F.; Ronco, Troels

    vast majority of infections, which may subsequently lead to serious neuropathologies such as Guillain-Barré syndrome. The aim of this study was to take advantage of whole genome sequencing (WGS) to in-depth characterize a subset of 16 C. jejuni and C. coli isolates from broilers from five farms....

  17. Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China.

    Science.gov (United States)

    Lu, Shan; Jin, Dong; Wu, Shusheng; Yang, Jing; Lan, Ruiting; Bai, Xiangning; Liu, Sha; Meng, Qiong; Yuan, Xuejiao; Zhou, Juan; Pu, Ji; Chen, Qiang; Dai, Hang; Hu, Yuanyuan; Xiong, Yanwen; Ye, Changyun; Xu, Jianguo

    2016-12-07

    Escherichia coli is both of a widespread harmless gut commensal and a versatile pathogen of humans. Domestic animals are a well-known reservoir for pathogenic E. coli. However, studies of E. coli populations from wild animals that have been separated from human activities had been very limited. Here we obtained 580 isolates from intestinal contents of 116 wild Marmot Marmota himalayana from Qinghai-Tibet plateau, China, with five isolates per animal. We selected 125 (hereinafter referred to as strains) from the 580 isolates for genome sequencing, based on unique pulse field gel electrophoresis patterns and at least one isolate per animal. Whole genome sequence analysis revealed that all 125 strains carried at least one and the majority (79.2%) carried multiple virulence genes based on the analysis of 22 selected virulence genes. In particular, the majority of the strains carried virulence genes from different pathovars as potential 'hybrid pathogens'. The alleles of eight virulence genes from the Marmot E. coli were found to have diverged earlier than all known alleles from human and other animal E. coli. Phylogenetic analysis of the 125 Marmot E. coli genomes and 355 genomes selected from 1622 human and other E. coli strains identified two new phylogroups, G and H, both of which diverged earlier than the other phylogroups. Eight of the 12 well-known pathogenic E. coli lineages were found to share a most recent common ancestor with one or more Marmot E. coli strains. Our results suggested that the intestinal E. coli of the Marmots contained a diverse virulence gene pool and is potentially pathogenic to humans. These findings provided a new understanding of the evolutionary origin of pathogenic E. coli.

  18. Influences of Globalization on K-12 Language Teacher Education Programs

    Science.gov (United States)

    Singh, Navin Kumar

    2012-01-01

    The purpose of this study was to explore the effects of globalization on K-12 language teacher education at Northern Arizona University (NAU) in terms of multilingual practices in the US, with reference to an English-only-state, Arizona. This study explored influences of globalization on K-12 language education practices in the US through teacher…

  19. Keeping Pace with K-12 Online Learning, 2016

    Science.gov (United States)

    Gemin, Butch; Pape, Larry

    2017-01-01

    "Keeping Pace with K-12 Online Learning 2016" marks the thirteenth consecutive year Evergreen has published its annual research of the K-12 education online learning market. The thirteen years of researching, writing and publishing this report represents a time of remarkable change. There has been a constant presence that has become the…

  20. Streptococcus salivarius K12 Limits Group B Streptococcus Vaginal Colonization.

    Science.gov (United States)

    Patras, Kathryn A; Wescombe, Philip A; Rösler, Berenice; Hale, John D; Tagg, John R; Doran, Kelly S

    2015-09-01

    Streptococcus agalactiae (group B streptococcus [GBS]) colonizes the rectovaginal tract in 20% to 30% of women and during pregnancy can be transmitted to the newborn, causing severe invasive disease. Current routine screening and antibiotic prophylaxis have fallen short of complete prevention of GBS transmission, and GBS remains a leading cause of neonatal infection. We have investigated the ability of Streptococcus salivarius, a predominant member of the native human oral microbiota, to control GBS colonization. Comparison of the antibacterial activities of multiple S. salivarius strains by use of a deferred-antagonism test showed that S. salivarius strain K12 exhibited the broadest spectrum of activity against GBS. K12 effectively inhibited all GBS strains tested, including disease-implicated isolates from newborns and colonizing isolates from the vaginal tract of pregnant women. Inhibition was dependent on the presence of megaplasmid pSsal-K12, which encodes the bacteriocins salivaricin A and salivaricin B; however, in coculture experiments, GBS growth was impeded by K12 independently of the megaplasmid. We also demonstrated that K12 adheres to and invades human vaginal epithelial cells at levels comparable to GBS. Inhibitory activity of K12 was examined in vivo using a mouse model of GBS vaginal colonization. Mice colonized with GBS were treated vaginally with K12. K12 administration significantly reduced GBS vaginal colonization in comparison to nontreated controls, and this effect was partially dependent on the K12 megaplasmid. Our results suggest that K12 may have potential as a preventative therapy to control GBS vaginal colonization and thereby prevent its transmission to the neonate during pregnancy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

    Science.gov (United States)

    Salipante, Stephen J.; Roach, David J.; Kitzman, Jacob O.; Snyder, Matthew W.; Stackhouse, Bethany; Butler-Wu, Susan M.; Lee, Choli; Cookson, Brad T.

    2015-01-01

    Large-scale bacterial genome sequencing efforts to date have provided limited information on the most prevalent category of disease: sporadically acquired infections caused by common pathogenic bacteria. Here, we performed whole-genome sequencing and de novo assembly of 312 blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous, consistent with pan-genome analyses encompassing the larger species. Investigation of differential virulence factor content and antibiotic resistance phenotypes reveals markedly different profiles among lineages and among strains infecting different body sites. We use high-resolution molecular epidemiology to explore the dynamics of infections at the level of individual patients, including identification of possible person-to-person transmission. Notably, a limited number of discrete lineages caused the majority of bloodstream infections, including one subclone (ST131-H30) responsible for 28% of bacteremic E. coli infections over a 3-yr period. We additionally use a microbial genome-wide-association study (GWAS) approach to identify individual genes responsible for antibiotic resistance, successfully recovering known genes but notably not identifying any novel factors. We anticipate that in the near future, whole-genome sequencing of microorganisms associated with clinical disease will become routine. Our study reveals what kind of information can be obtained from sequencing clinical isolates on a large scale, even well-characterized organisms such as E. coli, and provides insight into how this information might be utilized in a healthcare setting. PMID:25373147

  2. Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

    Science.gov (United States)

    Sims, Gregory E.; Kim, Sung-Hou

    2011-01-01

    A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects of E. coli/Shigella genomic evolution: (i) one based on the compositions of all possible features of length l = 24 (∼8.4 million features), which are likely to reveal the phenetic grouping and relationship among the organisms and (ii) the other based on the compositions of core features with low frequency and low variability (∼0.56 million features), which account for ∼69% of all commonly shared features among 38 taxa examined and are likely to have genome-wide lineal evolutionary signal. Shigella appears as a single clade when all possible features are used without filtering of noncore features. However, results using core features show that Shigella consists of at least two distantly related subclades, implying that the subclades evolved into a single clade because of a high degree of convergence influenced by mobile genetic elements and niche adaptation. In both FFP trees, the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that the E. coli/Shigella ancestor was likely a facultative or opportunistic pathogen. The extant commensal strains diverged relatively late and appear to be the result of reductive evolution of genomes. We also identify clade distinguishing features and their associated genomic regions within each phylogroup. Such features may provide useful information for understanding evolution of the groups and for quick diagnostic identification of each phylogroup. PMID:21536867

  3. The Glyphosate-Based Herbicide Roundup Does not Elevate Genome-Wide Mutagenesis of Escherichia coli

    Directory of Open Access Journals (Sweden)

    Clayton Tincher

    2017-10-01

    Full Text Available Mutations induced by pollutants may promote pathogen evolution, for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole-genome sequencing (MA/WGS method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH Roundup Concentrate Plus. The genome-wide mutation rate decreases as GBH concentration increases, suggesting that even long-term GBH exposure does not compromise the genome stability of bacteria.

  4. In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

    Directory of Open Access Journals (Sweden)

    Thaís C.G. Rojas

    2014-02-01

    Full Text Available Avian pathogenic Escherichia coli (APEC infections are responsible for significant losses in the poultry industry worldwide. A zoonotic risk has been attributed to APEC strains because they present similarities to extraintestinal pathogenic E. coli (ExPEC associated with illness in humans, mainly urinary tract infections and neonatal meningitis. Here, we present in silico analyses with pathogenic E. coli genome sequences, including recently available APEC genomes. The phylogenetic tree, based on multi-locus sequence typing (MLST of seven housekeeping genes, revealed high diversity in the allelic composition. Nevertheless, despite this diversity, the phylogenetic tree was able to cluster the different pathotypes together. An in silico virulence gene profile was also determined for each of these strains, through the presence or absence of 83 well-known virulence genes/traits described in pathogenic E. coli strains. The MLST phylogeny and the virulence gene profiles demonstrated a certain genetic similarity between Brazilian APEC strains, APEC isolated in the United States, UPEC (uropathogenic E. coli and diarrheagenic strains isolated from humans. This correlation corroborates and reinforces the zoonotic potential hypothesis proposed to APEC.

  5. Ongoing phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Akiko Kashiwagi

    2011-08-01

    Full Text Available According to the Red Queen hypothesis or arms race dynamics, coevolution drives continuous adaptation and counter-adaptation. Experimental models under simplified environments consisting of bacteria and bacteriophages have been used to analyze the ongoing process of coevolution, but the analysis of both parasites and their hosts in ongoing adaptation and counter-adaptation remained to be performed at the levels of population dynamics and molecular evolution to understand how the phenotypes and genotypes of coevolving parasite-host pairs change through the arms race. Copropagation experiments with Escherichia coli and the lytic RNA bacteriophage Qβ in a spatially unstructured environment revealed coexistence for 54 days (equivalent to 163-165 replication generations of Qβ and fitness analysis indicated that they were in an arms race. E. coli first adapted by developing partial resistance to infection and later increasing specific growth rate. The phage counter-adapted by improving release efficiency with a change in host specificity and decrease in virulence. Whole-genome analysis indicated that the phage accumulated 7.5 mutations, mainly in the A2 gene, 3.4-fold faster than in Qβ propagated alone. E. coli showed fixation of two mutations (in traQ and csdA faster than in sole E. coli experimental evolution. These observations suggest that the virus and its host can coexist in an evolutionary arms race, despite a difference in genome mutability (i.e., mutations per genome per replication of approximately one to three orders of magnitude.

  6. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome.

    Science.gov (United States)

    Clarke, L; Carbon, J

    1976-09-01

    Using the poly(dA-dT) "connector" method (Lobbanand Kaiser, 1973), a population of annealed hybrid circular DNAs was constructed in vitro; each hybrid DNA circle contained one molecule of poly(dT)-tailed Col El-DNA (LRI) annealed to any one of a collection of poly(dA)-tailed linear DNA fragments, produced originally by shearing total E. coli DNA to an average size of 8.5 x 10(6) daltons. This annealed DNA preparation (12 mug) was used to transform an F+ recA E. coli strain (JA200), selecting transformants by their resistance to colicin El. A collection or "bank" pf pver 2000 colicin El-resistant clones was thereby obtained, 70% of which were shown to contain hybrid Col El DNA (E. coli) plasmids. This colony bank is large enough to include hybrid plasmids representative of the entire E. coli genome. Individual plasmids have been readily identified by replica mating the collection onto plates seeded with cultures of various F- auxotrophic recipients, selecting for complementation of the auxotrophic markers by F-mediated transfer of hybrid plasmids to the F- recipients. In this manner, over 80 hybrid Col El-DNA (E. coli), plasmid-bearing clones have been identified in the colony bank, and about 40 known E. coli genes have been tentatively assigned to these various plasmids. The hybrid plasmids are transferred efficiently from F+ donors to appropriate F- recipients. The use of this method to establish similar colony banks in E. coli containing hybrid plasmids representative of various simple eucaryotic genomes is discussed.

  7. Biology and genomics of an historic therapeutic Escherichia coli bacteriophage collection

    DEFF Research Database (Denmark)

    Baig, Abiyad; Colom, Joan; Barrow, Paul

    2017-01-01

    We have performed microbiological and genomic characterization of an historic collection of nine bacteriophages, specifically infecting a K1 E. coli O18:K1:H7 ColV+ strain. These phages were isolated from sewage and tested for their efficacy in vivo for the treatment of systemic E. coli infection...... in a mouse infection model by Smith and Huggins (1982). The aim of the study was to identify common microbiological and genomic characteristics, which co-relate to the performance of these phages in in vivo study. These features will allow an informed selection of phages for use as therapeutic agents....... Transmission electron microscopy showed that six of the nine phages were Podoviridae and the remaining three were Siphoviridae. The four best performing phages in vivo belonged to the Podoviridae family. In vitro, these phages exhibited very short latent and rise periods in our study. In agreement...

  8. The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli

    DEFF Research Database (Denmark)

    Cho, Suhyung; Cho, Yoo-Bok; Kang, Taek Jin

    2015-01-01

    DNA-binding motifs that are recognized by transcription factors (TFs) have been well studied; however, challenges remain in determining the in vivo architecture of TF-DNA complexes on a genome-scale. Here, we determined the in vivo architecture of Escherichia coli arginine repressor (Arg...... facilitate the non-specific contacts between ArgR subunits and the residual sequences. Additionally, our approach may also reveal other fundamental structural features of TF-DNA interactions that have implications for studying genome-scale transcriptional regulatory networks....

  9. Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia.

    Science.gov (United States)

    Bernal, Johan F; Donado-Godoy, Pilar; Valencia, María Fernanda; León, Maribel; Gómez, Yolanda; Rodríguez, Fernando; Agarwala, Richa; Landsman, David; Mariño-Ramírez, Leonardo

    2016-03-17

    Campylobacter coli, along with Campylobacter jejuni, is a major agent of gastroenteritis and acute enterocolitis in humans. We report the whole-genome sequences of two multidrug-resistance C. coli strains, isolated from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and tetracycline. Copyright © 2016 Bernal et al.

  10. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

    Directory of Open Access Journals (Sweden)

    Marie Touchon

    2009-01-01

    Full Text Available The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re- annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species, including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an

  11. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

    Science.gov (United States)

    Touchon, Marie; Hoede, Claire; Tenaillon, Olivier; Barbe, Valérie; Baeriswyl, Simon; Bidet, Philippe; Bingen, Edouard; Bonacorsi, Stéphane; Bouchier, Christiane; Bouvet, Odile; Calteau, Alexandra; Chiapello, Hélène; Clermont, Olivier; Cruveiller, Stéphane; Danchin, Antoine; Diard, Médéric; Dossat, Carole; Karoui, Meriem El; Frapy, Eric; Garry, Louis; Ghigo, Jean Marc; Gilles, Anne Marie; Johnson, James; Le Bouguénec, Chantal; Lescat, Mathilde; Mangenot, Sophie; Martinez-Jéhanne, Vanessa; Matic, Ivan; Nassif, Xavier; Oztas, Sophie; Petit, Marie Agnès; Pichon, Christophe; Rouy, Zoé; Ruf, Claude Saint; Schneider, Dominique; Tourret, Jérôme; Vacherie, Benoit; Vallenet, David; Médigue, Claudine; Rocha, Eduardo P C; Denamur, Erick

    2009-01-01

    The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.

  12. Biochemical construction and selection of hybrid plasmids containing specific segments of the Escherichia coli genome.

    Science.gov (United States)

    Clarke, L; Carbon, J

    1975-11-01

    Using a poly(dA-dT) "connector" method, a population of annealed hybrid circular DNAs was constructed in vitro; each hybrid DNA circle containing one full-length molecule of poly(dT)-tailed DNA from E1 colicinogenic factor (Col E1) fragmented by EcoRI endonuclease annealed to any one of a collection of poly(dA)-tailed linear DNA fragments of the entire E. coli genome. This annealed, but unligated, hybrid DNA was used to transform several different auxotrophic mutants of E. coli, and by direct selection, bacterial clones were isolated which contained specific hybrid plasmids. In this manner, bacterial strains containing Col E1 hybrid plasmids carrying the entire tryptophan operon or the arabinsoe and leucine operons were isolated. The methods described should allow the molecular cloning of any portion of the E. coli genome by selection from a pool of DNA molecules containing at least several hundred different hybrids representing the entire bacterial genome.

  13. Undergraduate interest in K--12 teaching and the perceived 'climate' for the K--12 education profession in the natural sciences

    Science.gov (United States)

    Gerdeman, Robert Dean

    Previous research suggests that the natural science setting in universities does not offer a supportive environment for undergraduates interested in K--12 education careers, an important problem given the need for K--12 science teachers. A mixed-method approach was used to examine student perspectives toward K--12 education careers, and the influence of the college experience on perspectives, at a public research university. Quantitative data come from a cross-sectional survey sample (N = 444) of upper-division natural science majors in the university. The survey focused on student background characteristics, undergraduate experiences, perceptions of the college environment, career interests, and satisfaction. Pursuit of K--12 education as a top current career choice was rare among the respondents (3.6%). However, about one-fourth of them indicated some interest in this career and overall interest increased slightly during the college experience. Based on student perceptions, K--12 education was substantially less emphasized within the natural sciences than other career fields. Regression analyses revealed that the most important predictors (aside from initial career interests) of interest in and attitude toward K--12 teaching were self-concept and personality measures. Several college experience measures were also predictors, including perceptions about faculty and peers in the natural sciences. The effect of college experiences differed for students initially more inclined toward K--12 teaching, who reported a net decrease in interest, versus those more disinclined, who reported a net gain in interest. Satisfaction with the college experience was similar for the two groups. Qualitative data come from follow-up interviews conducted with eight survey respondents who recalled a top choice of K--12 teaching upon entering college but had decided to pursue another career. These students perceived other career fields to offer better professional opportunities for

  14. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

    OpenAIRE

    Ogura, Yoshitoshi; Ooka, Tadasuke; Iguchi, Atsushi; Toh, Hidehiro; Asadulghani, Md; Oshima, Kenshiro; Kodama, Toshio; Abe, Hiroyuki; Nakayama, Keisuke; Kurokawa, Ken; Tobe, Toru; Hattori, Masahira; Hayashi, Tetsuya

    2009-01-01

    Among the various pathogenic Escherichia coli strains, enterohemorrhagic E. coli (EHEC) is the most devastating. Although serotype O157:H7 strains are the most prevalent, strains of different serotypes also possess similar pathogenic potential. Here, we present the results of a genomic comparison between EHECs of serotype O157, O26, O111, and O103, as well as 21 other, fully sequenced E. coli/Shigella strains. All EHECs have much larger genomes (5.5–5.9 Mb) than the other strains and contain ...

  15. Comparative Genomics of Escherichia coli Isolated from Skin and Soft Tissue and Other Extraintestinal Infections

    Directory of Open Access Journals (Sweden)

    Amit Ranjan

    2017-08-01

    Full Text Available Escherichia coli, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs, meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs, and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic E. coli (ExPEC. It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive. In the study reported here, ExPEC E. coli isolated from SSTIs was characterized, including virulence and drug resistance profiles, and compared with isolates from patients suffering either pyelonephritis or septicemia. Results revealed that the majority of the isolates belonged to two pathogenic phylogroups, B2 and D. Approximately 67% of the isolates were multidrug resistant (MDR, with 85% producing extended-spectrum beta-lactamase (ESBL and 6% producing metallo-beta-lactamase (MBL. The blaCTX-M-15 genotype was observed in at least 70% of the E. coli isolates in each category, conferring resistance to an extended range of beta-lactam antibiotics. Whole-genome sequencing and comparative genomics of the ExPEC isolates revealed that two of the four isolates from SSTIs, NA633 and NA643, belong to pandemic sequence type ST131, whereas functional characteristics of three of the ExPEC pathotypes revealed that they had equal capabilities to form biofilm and were resistant to human serum. Overall, the isolates from a variety of ExPEC infections demonstrated similar resistomes and virulomes and did not display any disease-specific functional or genetic coordinates.

  16. Sequence periodicity of Escherichia coli is concentrated in intergenic regions

    Directory of Open Access Journals (Sweden)

    Trifonov Edward N

    2004-08-01

    Full Text Available Abstract Background Sequence periodicity with a period close to the DNA helical repeat is a very basic genomic property. This genomic feature was demonstrated for many prokaryotic genomes. The Escherichia coli sequences display the period close to 11 base pairs. Results Here we demonstrate that practically only ApA/TpT dinucleotides contribute to overall dinucleotide periodicity in Escherichia coli. The noncoding sequences reveal this periodicity much more prominently compared to protein-coding sequences. The sequence periodicity of ApC/GpT, ApT and GpC dinucleotides along the Escherichia coli K-12 is found to be located as well mainly within the intergenic regions. Conclusions The observed concentration of the dinucleotide sequence periodicity in the intergenic regions of E. coli suggests that the periodicity is a typical property of prokaryotic intergenic regions. We suppose that this preferential distribution of dinucleotide periodicity serves many biological functions; first of all, the regulation of transcription.

  17. Biology and Genomics of an Historic Therapeutic Escherichia coli Bacteriophage Collection

    Directory of Open Access Journals (Sweden)

    Abiyad Baig

    2017-08-01

    Full Text Available We have performed microbiological and genomic characterization of an historic collection of nine bacteriophages, specifically infecting a K1 E. coli O18:K1:H7 ColV+ strain. These phages were isolated from sewage and tested for their efficacy in vivo for the treatment of systemic E. coli infection in a mouse infection model by Smith and Huggins (1982. The aim of the study was to identify common microbiological and genomic characteristics, which co-relate to the performance of these phages in in vivo study. These features will allow an informed selection of phages for use as therapeutic agents. Transmission electron microscopy showed that six of the nine phages were Podoviridae and the remaining three were Siphoviridae. The four best performing phages in vivo belonged to the Podoviridae family. In vitro, these phages exhibited very short latent and rise periods in our study. In agreement with their microbiological profiles, characterization by genome sequencing showed that all six podoviruses belong to the Autographivirinae subfamily. Of these, four were isolates of the same species (99% identity, whereas two had divergent genomes compared to other podoviruses. The Siphoviridae phages, which were moderate to poor performers in vivo, exhibited longer latent and rise periods in vitro. Two of the three siphoviruses were closely related to each other (99% identity, but all can be associated with the Guernseyvirinae subfamily. Genome sequence comparison of both types of phages showed that a gene encoding for DNA-dependent RNA polymerase was only present in phages with faster replication cycle, which may account for their better performance in vivo. These data define a combination of microbiological, genomic and in vivo characteristics which allow a more rational evaluation of the original in vivo data and pave the way for the selection of phages for future phage therapy trails.

  18. DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins.

    Science.gov (United States)

    Milbredt, Sarah; Farmani, Neda; Sobetzko, Patrick; Waldminghaus, Torsten

    2016-10-21

    The standard outline of bacterial genomes is a single circular chromosome with a single replication origin. From the bioengineering perspective, it appears attractive to extend this basic setup. Bacteria with split chromosomes or multiple replication origins have been successfully constructed in the last few years. The characteristics of these engineered strains will largely depend on the respective DNA replication patterns. However, the DNA replication has not been investigated systematically in engineered bacteria with multiple origins or split replicons. Here we fill this gap by studying a set of strains consisting of (i) E. coli strains with an extra copy of the native replication origin (oriC), (ii) E. coli strains with an extra copy of the replication origin from the secondary chromosome of Vibrio cholerae (oriII), and (iii) a strain in which the E. coli chromosome is split into two linear replicons. A combination of flow cytometry, microarray-based comparative genomic hybridization (CGH), and modeling revealed silencing of extra oriC copies and differential timing of ectopic oriII copies compared to the native oriC. The results were used to derive construction rules for future multiorigin and multireplicon projects.

  19. Occurrence and Genomic Characterization of ESBL-Producing, MCR-1-Harboring Escherichia coli in Farming Soil

    Directory of Open Access Journals (Sweden)

    Beiwen Zheng

    2017-12-01

    Full Text Available The emergence and spread of the mobile colistin resistance gene (mcr-1 has become a major global public health concern. So far, this gene has been widely detected in food animals, pets, food, and humans. However, there is little information on the contamination of mcr-1-containing bacteria in farming soils. In August 2016, a survey of ESBL-producing Escherichia coli isolated from farming soils was conducted in Shandong Province, China. We observed colistin resistance in 12 of 53 (22.6% ESBL-producing Enterobacteriaceae isolates from farming soil. Six mcr-1-positive E. coli strains originating from a livestock-intensive area were found. The isolates belonged to four different STs (ST2060, ST3014, ST6756, and ST1560 and harbored extensive additional resistance genes. An E. coli with blaNDM-1 was also detected in a soil sample from the same area. Comparative whole genome sequencing and S1-PFGE analysis indicated that mcr-1 was chromosomally encoded in four isolates and located on IncHI2 plasmids in two isolates. To our knowledge, we report the first isolation of mcr-1 in ESBL-producing E. coli from farming soils. This work highlights the importance of active surveillance of colistin-resistant organisms in soil. Moreover, investigations addressing the influence of animal manure application on the transmission of mcr-1-producing bacteria are also warranted.

  20. Genome Editing in Escherichia coli with Cas9 and synthetic CRISPRs

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ze; Richardson, Sarah; Robinson, David; Deutsch, Samuel; Cheng, Jan-Fang

    2014-03-14

    Recently, the Cas9-CRISPR system has proven to be a useful tool for genome editing in eukaryotes, which repair the double stranded breaks made by Cas9 with non-homologous end joining or homologous recombination. Escherichia coli lacks non-homologous end joining and has a very low homologous recombination rate, effectively rendering targeted Cas9 activity lethal. We have developed a heat curable, serializable, plasmid based system for selectionless Cas9 editing in arbitrary E. coli strains that uses synthetic CRISPRs for targeting and -red to effect repairs of double stranded breaks. We have demonstrated insertions, substitutions, and multi-target deletions with our system, which we have tested in several strains.

  1. Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production

    Directory of Open Access Journals (Sweden)

    Yoon Byoung

    2009-01-01

    Full Text Available Abstract Background Deletion of large blocks of nonessential genes that are not needed for metabolic pathways of interest can reduce the production of unwanted by-products, increase genome stability, and streamline metabolism without physiological compromise. Researchers have recently constructed a reduced-genome Escherichia coli strain MDS42 that lacks 14.3% of its chromosome. Results Here we describe the reengineering of the MDS42 genome to increase the production of the essential amino acid L-threonine. To this end, we over-expressed a feedback-resistant threonine operon (thrA*BC, deleted the genes that encode threonine dehydrogenase (tdh and threonine transporters (tdcC and sstT, and introduced a mutant threonine exporter (rhtA23 in MDS42. The resulting strain, MDS-205, shows an ~83% increase in L-threonine production when cells are grown by flask fermentation, compared to a wild-type E. coli strain MG1655 engineered with the same threonine-specific modifications described above. And transcriptional analysis revealed the effect of the deletion of non-essential genes on the central metabolism and threonine pathways in MDS-205. Conclusion This result demonstrates that the elimination of genes unnecessary for cell growth can increase the productivity of an industrial strain, most likely by reducing the metabolic burden and improving the metabolic efficiency of cells.

  2. Media Literacy and the K-12 Content Areas

    Science.gov (United States)

    Hobbs, Renee

    2005-01-01

    Media literacy education is being explored by scholars in many different fields (including education, literature, media studies, psychology, and public health), but there is less evidence of implementations occurring in K-12 settings. With more than 1.3 million teachers in U.S. public schools, it is impossible to estimate the extent to which the…

  3. Information Security Management Practices of K-12 School Districts

    Science.gov (United States)

    Nyachwaya, Samson

    2013-01-01

    The research problem addressed in this quantitative correlational study was the inadequacy of sound information security management (ISM) practices in K-12 school districts, despite their increasing ownership of information assets. Researchers have linked organizational and sociotechnical factors to the implementation of information security…

  4. Engaging K-12 Language Learners in Media Literacy

    Science.gov (United States)

    Egbert, Joy; Neville, Chon

    2015-01-01

    Calls to integrate media literacy into K-12 language classrooms appear to have gone largely unheeded. However, media literacy skills are seen as crucial for 21st-century learners. This article answers the calls for a focus on media literacy in the language classroom by addressing both why and how systematic attention might be brought to this issue…

  5. Education Nation: Obama, Romney Outline Different K-12, Postsecondary Priorities

    Science.gov (United States)

    Dervarics, Charles

    2012-01-01

    With negative ads already rampant on radio and TV, it's clear that President Obama and Republican presidential nominee Mitt Romney differ on most issues. That statement carries over to education as well, as both offer starkly different views on K-12 and higher education policy for the fall campaign. Obama is touting a large increase in Pell Grants…

  6. Leadership Analysis in K-12 Case Study: "Divided Loyalties"

    Science.gov (United States)

    Alsubaie, Merfat Ayesh

    2016-01-01

    This report mainly aims to provide a critical and in-depth analysis of the K-12 Case, "Divided Loyalty" by Holy and Tartar (2004). The case recounts how the manifestation of inadequate leadership skills in a school setting could affect negatively the performance of students.

  7. Inspiring the Next Generation: Astronomy Catalyzes K12 STEM Education

    Science.gov (United States)

    Borders, Kareen; Thaller, Michelle; Winglee, Robert; Borders, Kyla

    2017-06-01

    K-12 educators need effective and relevant astronomy professional development. NASA's Mission Science provides innovative and accessible opportunities for K-12 teachers. Science questions involve scale and distance, including Moon/Earth scale, solar system scale, and distance of objects in the universe. Teachers can gain an understanding of basic telescopes, the history of telescopes, ground and satellite based telescopes, and models of JWST Telescope. An in-depth explanation of JWST and Spitzer telescopes gave participants background knowledge for infrared astronomy observations. During teacher training, we taught the electromagnetic spectrum through interactive stations. The stations included an overview via lecture and power point, the use of ultraviolet beads to determine ultraviolet exposure, the study of lenticulars and diagramming of infrared data, looking at visible light through diffraction glasses and diagramming the data, protocols for using astronomy based research in the classroom, and infrared thermometers to compare environmental conditions around the observatory. An overview of LIDAR physics was followed up by a simulated LIDAR mapping of the topography of Mars.We will outline specific steps for K-12 infrared astronomy professional development, provide data demonstrating the impact of the above professional development on educator understanding and classroom use, and detail future plans for additional K-12 professional development.Funding was provided by Washington STEM, NASA, and the Washington Space Grant Consortium.

  8. Transforming K-12 Rural Education through Blended Learning: Teacher Perspectives

    Science.gov (United States)

    Kellerer, Paula; Kellerer, Eric; Werth, Eric; Werth, Lori; Montgomery, Danielle; Clyde, Rozella; Cozart, Joe; Creach, Laura; Hibbard, Laura; LaFrance, Jason; Rupp, Nadine; Walker, Niki; Carter, Theresa; Kennedy, Kathryn

    2014-01-01

    A qualitative study exploring rural teacher perspectives on the impact of blended learning on students and teachers was conducted in Idaho during the Fall of 2013. Researchers from Northwest Nazarene University's DOCEO Center in partnership with Idaho Digital Learning Academy (IDLA) and the International Association for K-12 Online Learning…

  9. Green Power Partnership Top 30 K-12 Schools

    Science.gov (United States)

    The U.S. EPA's Green Power Partnership is a voluntary program designed to reduce the environmental impact of electricity generation by promoting renewable energy. On this list are the largest green power users among K-12 school partners within the GPP.

  10. Developing Open Education Literacies with Practicing K-12 Teachers

    Directory of Open Access Journals (Sweden)

    Royce M Kimmons

    2014-12-01

    Full Text Available This study seeks to understand how to use formal learning activities to effectively support the development of open education literacies among K-12 teachers. Considering pre- and post-surveys from K-12 teachers (n = 80 who participated in a three-day institute, this study considers whether participants entered institutes with false confidence or misconceptions related to open education, whether participant knowledge grew as a result of participation, whether takeaways matched expectations, whether time teaching (i.e., teacher veterancy impacted participant data, and what specific evaluation items influenced participants’ overall evaluations of the institutes. Results indicated that 1 participants entered the institutes with misconceptions or false confidence in several areas (e.g., copyright, fair use, 2 the institute was effective for helping to improve participant knowledge in open education areas, 3 takeaways did not match expectations, 4 time teaching did not influence participant evaluations, expectations, or knowledge, and 5 three specific evaluation items significantly influenced overall evaluations of the institute: learning activities, instructor, and website / online resources. Researchers conclude that this type of approach is valuable for improving K-12 teacher open education literacies, that various misconceptions must be overcome to support large-scale development of open education literacies in K-12, and that open education advocates should recognize that all teachers, irrespective of time teaching, want to innovate, utilize open resources, and share in an open manner.

  11. Project WILD Aquatic K-12 Curriculum and Activity Guide

    Science.gov (United States)

    Council for Environmental Education, 2011

    2011-01-01

    The "Project WILD Aquatic K-12 Curriculum and Activity Guide" emphasizes aquatic wildlife and aquatic ecosystems. It is organized in topic units and is based on the Project WILD conceptual framework. Because these activities are designed for integration into existing courses of study, instructors may use one or many Project WILD Aquatic activities…

  12. Exploring the Effectiveness of Online Education in K-12 Environments

    Science.gov (United States)

    Heafner, Tina L., Ed.; Hartshorne, Richard, Ed.; Petty, Teresa, Ed.

    2015-01-01

    The integration of technology in classrooms is rapidly emerging as a way to provide more educational opportunities for students. As virtual learning environments become more popular, evaluating the impact of this technology on student success is vital. "Exploring the Effectiveness of Online Education in K-12 Environments" combines…

  13. Designing GIS Learning Materials for K-12 Teachers

    Science.gov (United States)

    Hong, Jung Eun

    2017-01-01

    Although previous studies have proven the usefulness and effectiveness of geographic information system (GIS) use in the K-12 classroom, the rate of teacher adoption remains low. The identified major barrier to its use is a lack of teachers' background and experience. To solve this limitation, many organisations have provided GIS-related teacher…

  14. K-12 Marketplace Sees Major Flow of Venture Capital

    Science.gov (United States)

    Ash, Katie

    2012-01-01

    The flow of venture capital into the K-12 education market has exploded over the past year, reaching its highest transaction values in a decade in 2011, industry observers say. They attribute that rise to such factors as a heightened interest in educational technology; the decreasing cost of electronic devices such as tablet computers, laptops,…

  15. Best Practices in Administration of K-12 Dance Programs

    Science.gov (United States)

    Henneman, Suzanne E.

    2013-01-01

    The role of administering K-12 dance education programs is both exciting and invigorating. Being part of the decision-making process, problem solving with teams of colleagues, establishing routines and initiatives, creating "something from nothing," and watching programs grow is appealing to dance teachers as creative and critical…

  16. Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing.

    Science.gov (United States)

    Li, Yifan; Lin, Zhenquan; Huang, Can; Zhang, Yan; Wang, Zhiwen; Tang, Ya-Jie; Chen, Tao; Zhao, Xueming

    2015-09-01

    Engineering cellular metabolism for improved production of valuable chemicals requires extensive modulation of bacterial genome to explore complex genetic spaces. Here, we report the development of a CRISPR-Cas9 based method for iterative genome editing and metabolic engineering of Escherichia coli. This system enables us to introduce various types of genomic modifications with near 100% editing efficiency and to introduce three mutations simultaneously. We also found that cells with intact mismatch repair system had reduced chance to escape CRISPR mediated cleavage and yielded increased editing efficiency. To demonstrate its potential, we used our method to integrate the β-carotene synthetic pathway into the genome and to optimize the methylerythritol-phosphate (MEP) pathway and central metabolic pathways for β-carotene overproduction. We collectively tested 33 genomic modifications and constructed more than 100 genetic variants for combinatorially exploring the metabolic landscape. Our best producer contained15 targeted mutations and produced 2.0 g/L β-carotene in fed-batch fermentation. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  17. The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Jean-Philippe Côtôé

    2016-11-01

    Full Text Available Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. Of note, however, are the set of genes that become essential when bacteria are grown under nutrient stress. For example, more than 100 genes become indispensable when the model bacterium Escherichia coli is grown on nutrient-limited media, and many of these nutrient stress genes have also been shown to be important for the growth of various bacterial pathogens in vivo. To better understand the genetic network that underpins nutrient stress in E. coli, we performed a genome-scale cross of strains harboring deletions in some 82 nutrient stress genes with the entire E. coli gene deletion collection (Keio to create 315,400 double deletion mutants. An analysis of the growth of the resulting strains on rich microbiological media revealed an average of 23 synthetic sick or lethal genetic interactions for each nutrient stress gene, suggesting that the network defining nutrient stress is surprisingly complex. A vast majority of these interactions involved genes of unknown function or genes of unrelated pathways. The most profound synthetic lethal interactions were between nutrient acquisition and biosynthesis. Further, the interaction map reveals remarkable metabolic robustness in E. coli through pathway redundancies. In all, the genetic interaction network provides a powerful tool to mine and identify missing links in nutrient synthesis and to further characterize genes of unknown function in E. coli. Moreover, understanding of bacterial growth under nutrient stress could aid in the development of novel antibiotic discovery platforms.

  18. Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972

    DEFF Research Database (Denmark)

    Hancock, Viktoria; Seshasayee, Aswin S.; Ussery, David

    2008-01-01

    Escherichia coli strains are the major cause of urinary tract infections in humans. Such strains can be divided into virulent, UPEC strains causing symptomatic infections, and asymptomatic, commensal-like strains causing asymptomatic bacteriuria, ABU. The best-characterized ABU strain is strain...... factors for the human urinary tract could be identified. Also, presence/absence data of the gene expression was used as an adaptive genomics tool to model the gene pool of 83972 using primarily UPEC strain CFT073 as a scaffold. In our analysis, 96% of the transcripts filtered present in strain 83972 can...

  19. The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.

    Science.gov (United States)

    Ho, Wing Sze; Ou, Hong-Yu; Yeo, Chew Chieng; Thong, Kwai Lin

    2015-03-17

    Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd(+)) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd(+) E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands. The dndBCDE genes (dnd operon) were detected in all Dnd(+) E. coli strains by PCR. The addition of thiourea improved the typeability of Dnd(+) E. coli strains to 100% using PFGE and the Dnd(+) phenotype can be observed in both clonal and genetically diverse E. coli strains. Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two dnd operons were found within a strain although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E. coli although their link with virulence has not been explored. Genomic islands likely play an important role in facilitating the horizontal

  20. Genome-Wide Survey of Genes Under Positive Selection in Avian Pathogenic Escherichia coli Strains.

    Science.gov (United States)

    Rojas, Thaís Cabrera Galvão; Lobo, Francisco Pereira; Hongo, Jorge Augusto; Vicentini, Renato; Verma, Renu; Maluta, Renato Pariz; da Silveira, Wanderley Dias

    2017-05-01

    The ability to obtain bacterial genomes from the same host has allowed for comparative studies that help in the understanding of the molecular evolution of specific pathotypes. Avian pathogenic Escherichia coli (APEC) is a group of extraintestinal strains responsible for causing colibacillosis in birds. APEC is also suggested to possess a role as a zoonotic agent. Despite its importance, APEC pathogenesis still has several cryptic pathogenic processes that need to be better understood. In this work, a genome-wide survey of eight APEC strains for genes with evidence of recombination revealed that ∼14% of the homologous groups evaluated present signs of recombination. Enrichment analyses revealed that nine Gene Ontology (GO) terms were significantly more represented in recombinant genes. Among these GO terms, several were noted to be ATP-related categories. The search for positive selection in these APEC genomes revealed 32 groups of homologous genes with evidence of positive selection. Among these groups, we found several related to cell metabolism, as well as several uncharacterized genes, beyond the well-known virulence factors ompC, lamB, waaW, waaL, and fliC. A GO term enrichment test showed a prevalence of terms related to bacterial cell contact with the external environment (e.g., viral entry into host cell, detection of virus, pore complex, bacterial-type flagellum filament C, and porin activity). Finally, the genes with evidence of positive selection were retrieved from genomes of non-APEC strains and tested as were done for APEC strains. The result revealed that none of the groups of genes presented evidence of positive selection, confirming that the analysis was effective in inferring positive selection for APEC and not for E. coli in general, which means that the study of the genes with evidence of positive selection identified in this study can contribute for the better understanding of APEC pathogenesis processes.

  1. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

    DEFF Research Database (Denmark)

    Joensen, Katrine Grimstrup; Tetzschner, Anna M. M.; Iguchi, Atsushi

    2015-01-01

    typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-based in silico serotyping of E. coli applicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing...... was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org). All E. coli isolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE...... tool. SerotypeFinder was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen genes wzx, wzy, wzm, and wzt and the flagellin...

  2. Common and specific genomic sequences of avian and human extraintestinal pathogenic Escherichia coli as determined by genomic subtractive hybridization

    Directory of Open Access Journals (Sweden)

    Nolan Lisa K

    2007-08-01

    Full Text Available Abstract Background Suppression subtractive hybridization (SSH strategy was used with extraintestinal pathogenic Escherichia coli (EXPEC that cause avian colibacillosis (avian pathogenic E. coli or APEC and human urinary tract infections (uropathogenic E. coli or UPEC to determine if they possessed genes that were host and/or niche specific. Both APEC and UPEC isolates were used as tester and driver strains in 4 different SSHs in order to obtain APEC- and UPEC-specific subtraction fragments (SFs. Results These procedures yielded a total of 136 tester-specific SFs of which 85 were APEC-derived and 51 were UPEC-derived. Most of the APEC-derived SFs were associated with plasmids; whereas, the majority of UPEC-derived sequences matched to the bacterial chromosome. We further determined the distribution of these tester-derived sequences in a collection of UPEC and APEC isolates using polymerase chain reaction techniques. Plasmid-borne, APEC-derived sequences (tsh, cvaB, traR, traC and sopB were predominantly present in APEC, as compared to UPEC. Of the UPEC-derived SFs, those encoding hemolysin D and F1C major and minor fimbrial subunits were present only in UPEC. However, two UPEC-derived SFs that showed strong similarity to the uropathgenic-specific protein gene (usp occurred in APEC, demonstrating that usp is not specific to UPEC. Conclusion This study provides evidence of the genetic variability of ExPEC as well as genomic similarities between UPEC and APEC; it did not identify any single marker that would dictate host and/or niche specificity in APEC or UPEC. However, further studies on the genes that encode putative or hypothetical proteins might offer important insight into the pathogenesis of disease, as caused by these two ExPEC.

  3. Whole-Genome Characterization and Strain Comparison of VT2f-Producing Escherichia coli Causing Hemolytic Uremic Syndrome

    Science.gov (United States)

    Michelacci, Valeria; Bondì, Roslen; Gigliucci, Federica; Franz, Eelco; Badouei, Mahdi Askari; Schlager, Sabine; Minelli, Fabio; Tozzoli, Rosangela; Caprioli, Alfredo; Morabito, Stefano

    2016-01-01

    Verotoxigenic Escherichia coli infections in humans cause disease ranging from uncomplicated intestinal illnesses to bloody diarrhea and systemic sequelae, such as hemolytic uremic syndrome (HUS). Previous research indicated that pigeons may be a reservoir for a population of verotoxigenic E. coli producing the VT2f variant. We used whole-genome sequencing to characterize a set of VT2f-producing E. coli strains from human patients with diarrhea or HUS and from healthy pigeons. We describe a phage conveying the vtx2f genes and provide evidence that the strains causing milder diarrheal disease may be transmitted to humans from pigeons. The strains causing HUS could derive from VT2f phage acquisition by E. coli strains with a virulence genes asset resembling that of typical HUS-associated verotoxigenic E. coli. PMID:27584691

  4. Technical Feasibility Study for Zero Energy K-12 Schools

    Energy Technology Data Exchange (ETDEWEB)

    Bonnema, Eric [National Renewable Energy Lab. (NREL), Golden, CO (United States); Goldwasser, David [National Renewable Energy Lab. (NREL), Golden, CO (United States); Torcellini, Paul [National Renewable Energy Lab. (NREL), Golden, CO (United States); Pless, Shanti [National Renewable Energy Lab. (NREL), Golden, CO (United States); Studer, Daniel [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-11-01

    This technical feasibility study provides documentation and research results supporting a possible set of strategies to achieve source zero energy K-12 school buildings as defined by the U.S. Department of Energy (DOE) zero energy building (ZEB) definition (DOE 2015a). Under this definition, a ZEB is an energy-efficient building in which, on a source energy basis, the actual annual delivered energy is less than or equal to the on-site renewable exported energy.

  5. Exploring the combinatorial genomic space in Escherichia coli for ethanol tolerance.

    Science.gov (United States)

    Nicolaou, Sergios A; Gaida, Stefan M; Papoutsakis, Eleftherios T

    2012-11-01

    Strain tolerance to toxic chemicals is desirable for biologically producing biofuels and chemicals. Standard genomic libraries can be screened to identify genes imparting tolerance, but cannot capture interactions among proximal or distant loci. In search of ethanol tolerance determinants, we expanded the genomic space combinatorially by screening coexisting genomic libraries (CoGeLs) of fosmids (large inserts) and plasmids (smaller inserts) under increasing ethanol concentrations. Such screening led to identification of interacting genetic loci imparting ethanol tolerance. One pair of fragments ([galT, galE] and [recA, pncC, mltB]) increased survival under 50 g/L ethanol by 38% when coexpressed, but individually the fragments had no effect. Coexpression of two genomic fragments ([sfsB, murA, yrbA, mlaB, mlaC, mlaD, mlaE, mlaF, yrbG] and [yrbA, mlaB, mlaC]) enhanced Escherichia coli survival to 50 g/L ethanol by up to 115%. A 35-kb fosmid fragment increased tolerance to 63 g/L ethanol by 160%. While the tolerance levels of these strains compare favorably to or exceed the performance of previously reported engineered strains, more significantly, this study demonstrates that combinatorial library screening and screening fosmid libraries offer new, previously unexplored tools for identifying genetic determinants of ethanol, and by extrapolation, other alcohol tolerance. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Genome-wide mapping of furfural tolerance genes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Tirzah Y Glebes

    Full Text Available Advances in genomics have improved the ability to map complex genotype-to-phenotype relationships, like those required for engineering chemical tolerance. Here, we have applied the multiSCale Analysis of Library Enrichments (SCALEs; Lynch et al. (2007 Nat. Method. approach to map, in parallel, the effect of increased dosage for >10(5 different fragments of the Escherichia coli genome onto furfural tolerance (furfural is a key toxin of lignocellulosic hydrolysate. Only 268 of >4,000 E. coli genes (∼ 6% were enriched after growth selections in the presence of furfural. Several of the enriched genes were cloned and tested individually for their effect on furfural tolerance. Overexpression of thyA, lpcA, or groESL individually increased growth in the presence of furfural. Overexpression of lpcA, but not groESL or thyA, resulted in increased furfural reduction rate, a previously identified mechanism underlying furfural tolerance. We additionally show that plasmid-based expression of functional LpcA or GroESL is required to confer furfural tolerance. This study identifies new furfural tolerant genes, which can be applied in future strain design efforts focused on the production of fuels and chemicals from lignocellulosic hydrolysate.

  7. Determination of membrane disruption and genomic DNA binding of cinnamaldehyde to Escherichia coli by use of microbiological and spectroscopic techniques.

    Science.gov (United States)

    He, Tian-Fu; Zhang, Zhi-Hong; Zeng, Xin-An; Wang, Lang-Hong; Brennan, Charles S

    2018-01-01

    This work was aimed to investigate the antibacterial action of cinnamaldehyde (CIN) against Escherichia coli ATCC 8735 (E. coli) based on membrane fatty acid composition analysis, alterations of permeability and cell morphology as well as interaction with genomic DNA. Analysis of membrane fatty acids using gas chromatography-mass spectrometry (GC-MS) revealed that the proportion of unsaturated fatty acids (UFA) and saturated fatty acids (SFA) were the major fatty acids in plasmic membrane, and their levels were significantly changed after exposure of E. coli to CIN at low concentrations. For example, the proportion of UFA decreased from 39.97% to 20.98%, while the relative content of SFA increased from 50.14% to 67.80% as E. coli was grown in increasing concentrations of CIN (from 0 to 0.88mM). Scanning electron microscopy (SEM) showed that the morphology of E. coli cells to be wrinkled, distorted and even lysed after exposure to CIN, which therefore decreased the cell viability. The binding of CIN to genomic DNA was probed using fluorescence, UV-Visible absorption spectra, circular dichroism, molecular modeling and atomic force microscopy (AFM). Results indicated that CIN likely bound to the minor groove of genomic DNA, and changed the secondary structure and morphology of this biomacromolecule. Therefore, CIN can be deem as a kind of natural antimicrobial agents, which influence both cell membrane and genomic DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Genome sequences of thirty Escherichia coli O157:H7 isolates recovered from a single dairy farm and its associated off-site heifer raising facility

    Science.gov (United States)

    Cattle are the primary reservoir of Escherichia coli O157:H7, the most frequently isolated serotype of enterohemorrhagic E. coli infections among humans in North America. To evaluate the diversity of E. coli O157:H7 isolates within a single dairy herd the genomes of 30 isolates collected over a 7-ye...

  9. Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n-Butanol Production in Escherichia coli

    DEFF Research Database (Denmark)

    Heo, Min-Ji; Jung, Hwi-Min; Um, Jaeyong

    2017-01-01

    Genome editing using CRISPR/Cas9 was successfully demonstrated in Esherichia coli to effectively produce n-butanol in a defined medium under microaerobic condition. The butanol synthetic pathway genes including those encoding oxygen-tolerant alcohol dehydrogenase were overexpressed in metabolically...... prediction program, UTR designer, and modified using the CRISPR/Cas9 genome editing method to reduce its expression level. E. coli strains with decreased citrate synthase expression produced more butanol and the citrate synthase activity was correlated with butanol production. These results demonstrate...

  10. Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences.

    Science.gov (United States)

    Chattaway, Marie A; Schaefer, Ulf; Tewolde, Rediat; Dallman, Timothy J; Jenkins, Claire

    2017-02-01

    Escherichia coli and Shigella species are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species of Shigella are therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982 Escherichia coli and Shigella sp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasive E. coli isolates that were misidentified as Shigella flexneri or S. boydii by the kmer ID, and 8 were S. flexneri isolates misidentified by TB&S as S. boydii due to nonfunctional S. flexneri O antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising both S. boydii and S. dysenteriae strains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data. Shigella can be differentiated from E. coli and accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species of Shigella, and identified emerging pathoadapted lineages. © Crown copyright 2017.

  11. Involving Practicing Scientists in K-12 Science Teacher Professional Development

    Science.gov (United States)

    Bertram, K. B.

    2011-12-01

    The Science Teacher Education Program (STEP) offered a unique framework for creating professional development courses focused on Arctic research from 2006-2009. Under the STEP framework, science, technology, engineering, and math (STEM) training was delivered by teams of practicing Arctic researchers in partnership with master teachers with 20+ years experience teaching STEM content in K-12 classrooms. Courses based on the framework were offered to educators across Alaska. STEP offered in-person summer-intensive institutes and follow-on audio-conferenced field-test courses during the academic year, supplemented by online scientist mentorship for teachers. During STEP courses, teams of scientists offered in-depth STEM content instruction at the graduate level for teachers of all grade levels. STEP graduate-level training culminated in the translation of information and data learned from Arctic scientists into standard-aligned lessons designed for immediate use in K-12 classrooms. This presentation will focus on research that explored the question: To what degree was scientist involvement beneficial to teacher training and to what degree was STEP scientist involvement beneficial to scientist instructors? Data sources reveal consistently high levels of ongoing (4 year) scientist and teacher participation; high STEM content learning outcomes for teachers; high STEM content learning outcomes for students; high ratings of STEP courses by scientists and teachers; and a discussion of the reasons scientists indicate they benefited from STEP involvement. Analyses of open-ended comments by teachers and scientists support and clarify these findings. A grounded theory approach was used to analyze teacher and scientist qualitative feedback. Comments were coded and patterns analyzed in three databases. The vast majority of teacher open-ended comments indicate that STEP involvement improved K-12 STEM classroom instruction, and the vast majority of scientist open-ended comments

  12. Draft Genome Sequences of Escherichia coli Strains Isolated at Calving from the Uterus, Vagina, Vulva, and Rectoanal Junction of a Dairy Cow That Later Developed Metritis

    OpenAIRE

    Jeon, Soo Jin; Cunha, Federico; Ginn, Amber; Jeong, KwangCheol Casey; Galv?o, Klibs N.

    2017-01-01

    ABSTRACT Escherichia coli is involved in the pathogenicity of metritis in cows. We report here the genome sequences of E.?coli strains isolated at calving from the uterus, vagina, vulva, and rectoanal junction of a dairy cow that later developed metritis. The genomic similarities will give an insight into phylogenetic relationships among strains.

  13. Infrared Astronomy Professional Development for K-12 Educators: WISE Telescope

    Science.gov (United States)

    Borders, Kareen; Mendez, B. M.

    2010-01-01

    K-12 educators need effective and relevant astronomy professional development. WISE Telescope (Wide-Field Infrared Survey Explorer) and Spitzer Space Telescope Education programs provided an immersive teacher professional development workshop at Arecibo Observatory in Puerto Rico during the summer of 2009. As many common misconceptions involve scale and distance, teachers worked with Moon/Earth scale, solar system scale, and distance of objects in the universe. Teachers built and used basic telescopes, learned about the history of telescopes, explored ground and satellite based telescopes, and explored and worked on models of WISE Telescope. An in-depth explanation of WISE and Spitzer telescopes gave participants background knowledge for infrared astronomy observations. We taught the electromagnetic spectrum through interactive stations. The stations included an overview via lecture and power point, the use of ultraviolet beads to determine ultraviolet exposure, the study of WISE lenticulars and diagramming of infrared data, listening to light by using speakers hooked up to photoreceptor cells, looking at visible light through diffraction glasses and diagramming the data, protocols for using astronomy based research in the classroom, and infrared thermometers to compare environmental conditions around the observatory. An overview of LIDAR physics was followed up by a simulated LIDAR mapping of the topography of Mars. We will outline specific steps for K-12 infrared astronomy professional development, provide data demonstrating the impact of the above professional development on educator understanding and classroom use, and detail future plans for additional K-12 professional development. Funding was provided by WISE Telescope, Spitzer Space Telescope, Starbucks, Arecibo Observatory, the American Institute of Aeronautics and Astronautics, and the Washington Space Grant Consortium.

  14. AIAA Educator Academy: Enriching STEM Education for K-12 Students

    Science.gov (United States)

    Slagle, E.; Bering, E. A.; Longmier, B. W.; Henriquez, E.; Milnes, T.; Wiedorn, P.; Bacon, L.

    2012-12-01

    Educator Academy is a K-12 STEM curriculum developed by the STEM K-12 Outreach Committee of the American Institute of Aeronautics and Astronautics (AIAA). Consisting of three independent curriculum modules, K-12 students participate in inquiry-based engineering challenges to improve critical thinking skills and enhance problem solving skills. The Mars Rover Celebration Curriculum Module is designed for students in grades 3-8. Throughout this module, students learn about Mars and the solar system. Working with given design criteria, students work in teams to do basic research about Mars that will determine the operational objectives and structural features of their rover. Then, students participate in the design and construction of a model of a mock-up Mars Rover to carry out a specific science mission on the surface of Mars. At the end of this project, students have the opportunity to participate in a regional capstone event where students share their rover designs and what they have learned. The Electric Cargo Plan Curriculum Module is designed for students in grades 6-12. Throughout this module, students learn about aerodynamics and the four forces of flight. Working individually or in teams, students design and construct an electrically-powered model aircraft to fly a tethered flight of at least one lap without cargo, followed by a second tethered flight of one lap carrying as much cargo as possible. At the end of this project, students have the opportunity to participate in a regional capstone event where students share what they have learned and compete with their different cargo plane designs. The Space Weather Balloon Curriculum Module is designed for students in grades 9-12. Throughout this module, students learn and refine physics concepts as well as experimental research skills. Students participate in project-based learning that is experimental in nature. Students are engaged with the world around them as they collaborate to launch a high altitude

  15. Virulence potential and genomic mapping of the worldwide clone Escherichia coli ST131.

    Directory of Open Access Journals (Sweden)

    Jean-Philippe Lavigne

    Full Text Available Recently, the worldwide propagation of clonal CTX-M-15-producing Escherichia coli isolates, namely ST131 and O25b:H4, has been reported. Like the majority of extra-intestinal pathogenic E. coli isolates, the pandemic clone ST131 belongs to phylogenetic group B2, and has recently been shown to be highly virulent in a mouse model, even though it lacks several genes encoding key virulence factors (Pap, Cnf1 and HlyA. Using two animal models, Caenorhabditis elegans and zebrafish embryos, we assessed the virulence of three E. coli ST131 strains (2 CTX-M-15- producing urine and 1 non-ESBL-producing faecal isolate, comparing them with five non-ST131 B2 and a group A uropathogenic E. coli (UPEC. In C. elegans, the three ST131 strains showed intermediate virulence between the non virulent group A isolate and the virulent non-ST131 B2 strains. In zebrafish, the CTX-M-15-producing ST131 UPEC isolates were also less virulent than the non-ST131 B2 strains, suggesting that the production of CTX-M-15 is not correlated with enhanced virulence. Amongst the non-ST131 B2 group isolates, variation in pathogenic potential in zebrafish embryos was observed ranging from intermediate to highly virulent. Interestingly, the ST131 strains were equally persistent in surviving embryos as the non-ST131-group B2 strains, suggesting similar mechanisms may account for development of persistent infection. Optical maps of the genome of the ST131 strains were compared with those of 24 reference E. coli strains. Although small differences were seen within the ST131 strains, the tree built on the optical maps showed that these strains belonged to a specific cluster (86% similarity with only 45% similarity with the other group B2 strains and 25% with strains of group A and D. Thus, the ST131 clone has a genetic composition that differs from other group B2 strains, and appears to be less virulent than previously suspected.

  16. Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes

    OpenAIRE

    Ogura, Yoshitoshi; Ooka, Tadasuke; Asadulghani,; Terajima, Jun; Nougayr?de, Jean-Philippe; Kurokawa, Ken; Tashiro, Kousuke; Tobe, Toru; Nakayama, Keisuke; Kuhara, Satoru; Oswald, Eric; Watanabe, Haruo; Hayashi, Tetsuya

    2007-01-01

    Background: Enterohemorrhagic Escherichia coli (EHEC) O157 causes severe food-borne illness in humans. The chromosome of O157 consists of 4.1 Mb backbone sequences shared by benign E. coli K-12, and 1.4 Mb O157-specific sequences encoding many virulence determinants, such as Shiga toxin genes (stx genes) and the locus of enterocyte effacement (LEE). Non-O157 EHECs belonging to distinct clonal lineages from O157 also cause similar illness in humans. According to the "parallel" evolution model,...

  17. Draft genome sequence analysis of multidrug-resistant Escherichia coli strains isolated in 2013 from humans and chickens in Nigeria.

    Science.gov (United States)

    Here, we present the draft genome sequences of nine multidrug-resistant Escherichia coli isolated from humans (n=6) and chicken carcass (n=3) from Lagos, Nigeria in 2013. Multiple extended-spectrum beta-lactamase (ESBL) genes were identified in these isolates. ...

  18. Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain E24377A, Obtained from a Tribal Drinking Water Source in India.

    Science.gov (United States)

    Tamhankar, Ashok J; Nerkar, Sandeep S; Khadake, Prashant P; Akolkar, Dadasaheb B; Apurwa, Sachin R; Deshpande, Uday; Khedkar, Smita U; Stålsby-Lundborg, Cecilia

    2015-04-02

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in humans and animals. Its dissemination can occur through water sources contaminated by it. Here, we report for the first time the draft genome sequence of ETEC strain E24377A, obtained from a tribal drinking water source in India. Copyright © 2015 Tamhankar et al.

  19. Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain E24377A, Obtained from a Tribal Drinking Water Source in India

    OpenAIRE

    Tamhankar, Ashok J.; Nerkar, Sandeep S.; Khadake, Prashant P.; Akolkar, Dadasaheb B.; Apurwa, Sachin R.; Deshpande, Uday; Khedkar, Smita U.; St?lsby-Lundborg, Cecilia

    2015-01-01

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in humans and animals. Its dissemination can occur through water sources contaminated by it. Here, we report for the first time the draft genome sequence of ETEC strain E24377A, obtained from a tribal drinking water source in India.

  20. Draft Genome Sequences of Two Avian Pathogenic Escherichia coli Strains of Clinical Importance, E44 and E51

    DEFF Research Database (Denmark)

    Ronco, Troels; Stegger, Marc; Andersen, Paal S

    2016-01-01

    Avian pathogenic Escherichia coli strains have remarkable impacts on animal welfare and the production economy in the poultry industry worldwide. Here, we present the draft genomes of two isolates from chickens (E44 and E51) obtained from field outbreaks and subsequently investigated...

  1. The importance of terminology in teaching K-12 science

    Science.gov (United States)

    Yager, Robert E.

    Several recent reports concerning the status of science education in K-12 classrooms have emphasized the centrality of textbooks to instruction. Some initial investigations of the nature of textbooks have suggested that typically more new words and terms are introduced than one would expect to find in a similar time frame as foreign languages are studied. This is a review of these initial studies, a review of the studies of mastery of vocabulary in foreign languages, and a review of general research concerning the vocabulary development, especially as it pertains to reading. Twenty-five of the most commonly used textbooks in K-12 science classrooms are analyzed in terms of the occurrence of special/technical words. The number of words introduced at every level is considerable-often more than would be required if a new language were being introduced. In addition, the number of new words in science often approaches the total number that could be expected in terms of total vocabulary increase at a given grade level for a given student. There is strong evidence that one major fact of the current crisis in science education is the considerable emphasis upon words/terms/definitions as the primary ingredient of science-at least the science that a typical student encounters and that he/she is expected to master.

  2. A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Olin K Silander

    2012-01-01

    Full Text Available Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as "phenotypic noise." In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alone.

  3. Several pathways of hydrogen peroxide action that damage the E. coli genome

    Directory of Open Access Journals (Sweden)

    Nasser Ribeiro Asad

    2004-01-01

    Full Text Available Hydrogen peroxide is an important reactive oxygen species (ROS that arises either during the aerobic respiration process or as a by-product of water radiolysis after exposure to ionizing radiation. The reaction of hydrogen peroxide with transition metals imposes on cells an oxidative stress condition that can result in damage to cell components such as proteins, lipids and principally to DNA, leading to mutagenesis and cell death. Escherichia coli cells are able to deal with these adverse events via DNA repair mechanisms, which enable them to recover their genome integrity. These include base excision repair (BER, nucleotide excision repair (NER and recombinational repair. Other important defense mechanisms present in Escherichia coli are OxyR and SosRS anti-oxidant inducible pathways, which are elicited by cells to avoid the introduction of oxidative lesions by hydrogen peroxide. This review summarizes the phenomena of lethal synergism between UV irradiation (254 nm and H2O2, the cross-adaptive response between different classes of genotoxic agents and hydrogen peroxide, and the role of copper ions in the lethal response to H2O2 under low-iron conditions.

  4. Engineering Escherichia coli for poly-(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis.

    Science.gov (United States)

    Zheng, Yangyang; Yuan, Qianqian; Yang, Xiaoyan; Ma, Hongwu

    2017-11-01

    Poly-(3-hydroxybutyrate) (P3HB) is a promising biodegradable plastic synthesized from acetyl-CoA. One important factor affecting the P3HB production cost is the P3HB yield. Through flux balance analysis of an extended genome-scale metabolic network of E. coli, we found that the introduction of non-oxidative glycolysis pathway (NOG), a previously reported pathway enabling complete carbon conservation, can increase the theoretical carbon yield from 67% to 89%, equivalent to the theoretical mass yield from 0.48g P3HB/g glucose to 0.64g P3HB/g glucose. Based on this analysis result, we introduced phosphoketolase and enhanced the NOG pathway in E. coli. The mass yield in the engineered strain was increased from 0.16g P3HB/g glucose to 0.24g P3HB/g glucose. We further overexpressed pntAB to enhance the NADPH availability and down-regulated TCA cycle to divert more acetyl-CoA toward P3HB. The final construct accumulated 5.7g/L P3HB and reached a carbon yield of 0.43 (a mass yield of 0.31g P3HB/g glucose) in shake flask cultures in shake flask cultures. The introduction of NOG pathway could also be useful for improving yields of many other biochemicals derived from acetyl-coA. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Escherichia coli genome-scale metabolic gene knockout of lactate dehydrogenase (ldhA), increases succinate production from glycerol.

    Science.gov (United States)

    Mienda, Bashir Sajo

    2017-11-06

    Genome-scale metabolic model (GEM) of Escherichia coli has been published with applications in predicting metabolic engineering capabilities on different carbon sources and directing biological discovery. The use of glycerol as an alternative carbon source is economically viable in biorefinery. The use of GEM for predicting metabolic gene deletion of lactate dehydrogenase (ldhA) for increasing succinate production in Escherichia coli from glycerol carbon source remained largely unexplored. Here, I hypothesized that metabolic gene knockout of ldhA in E. coli from glycerol could increase succinate production. A proof-of-principle strain was constructed and designated as E. coli BMS5 (ΔldhA), by predicting increased succinate production in E. coli GEM and confirmed the predicted outcomes using wet cell experiments. The mutant GEM (ΔldhA) predicted 11% increase in succinate production from glycerol compared to its wild-type model (iAF1260), and the E. coli BMS5 (ΔldhA) showed 1.05 g/l and its corresponding wild-type produced .05 g/l (23-fold increase). The proof-of-principle strain constructed in this study confirmed the aforementioned hypothesis and further elucidated the fact that E. coli GEM can prospectively and effectively predict metabolic engineering interventions using glycerol as substrate and could serve as platform for new strain design strategies and biological discovery.

  6. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand.

    Science.gov (United States)

    Runcharoen, Chakkaphan; Raven, Kathy E; Reuter, Sandra; Kallonen, Teemu; Paksanont, Suporn; Thammachote, Jeeranan; Anun, Suthatip; Blane, Beth; Parkhill, Julian; Peacock, Sharon J; Chantratita, Narisara

    2017-09-06

    Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin. Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.

  7. Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California.

    Science.gov (United States)

    Worley, Jay N; Flores, Kristopher A; Yang, Xun; Chase, Jennifer A; Cao, Guojie; Tang, Shuai; Meng, Jianghong; Atwill, Edward R

    2017-08-15

    Escherichia coli serotype O157:H7 is a zoonotic food- and waterborne bacterial pathogen that causes a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, such as cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle presents food safety challenges on a uniquely large scale. We performed a survey of E. coli O157:H7 on 20 farms in California to observe the regional diversity and prevalence of E. coli O157:H7. Isolates were obtained from enrichment cultures of cow feces. Some farms were sampled on two dates. Genomes from isolates were sequenced to determine their relatedness and pathogenic potential. E. coli O157:H7 was isolated from approximately half of the farms. The point prevalence of E. coli O157:H7 on farms was highly variable, ranging from zero to nearly 90%. Within farms, generally one or a few lineages were found, even when the rate of isolation was high. On farms with high isolation rates, a single clonal lineage accounted for most of the isolates. Farms that were visited months after the first visit might have had the same lineages of E. coli O157:H7. Strains of E. coli O157:H7 may be persistent for months on farms. IMPORTANCE This survey of 20 cow-calf operations from different regions of California provides an in depth look at resident Escherichia coli O157:H7 populations at the molecular level. E. coli O157:H7 is found to have a highly variable prevalence, and with whole-genome sequencing, high prevalences in herds were found to be due to a single lineage shed from multiple cows. Few repeat lineages were found between farms in this area; therefore, we predict that E. coli O157:H7 has significant diversity in this area beyond what is detected in this survey. All

  8. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data.

    Science.gov (United States)

    Joensen, Katrine G; Tetzschner, Anna M M; Iguchi, Atsushi; Aarestrup, Frank M; Scheutz, Flemming

    2015-08-01

    Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. Conventional serotyping of Escherichia coli is a delicate, laborious, time-consuming, and expensive procedure. With whole-genome sequencing (WGS) becoming cheaper, it has vast potential in routine typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-based in silico serotyping of E. coli applicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org). All E. coli isolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE tool. SerotypeFinder was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen genes wzx, wzy, wzm, and wzt and the flagellin genes fliC, flkA, fllA, flmA, and flnA were detected in 569 and 508 genome sequences, respectively. SerotypeFinder for WGS-based O and H typing predicted 560 of 569 O types and 504 of 508 H types, consistent with conventional serotyping. In combination with other available WGS typing tools, E. coli serotyping can be performed solely from WGS data, providing faster and cheaper typing than current routine procedures and making WGS typing a superior alternative to conventional typing strategies. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. Scarless Cas9 Assisted Recombineering (no-SCAR) in Escherichia coli, an Easy-to-Use System for Genome Editing.

    Science.gov (United States)

    Reisch, Christopher R; Prather, Kristala L J

    2017-01-05

    The discovery and development of genome editing systems that leverage the site-specific DNA endonuclease system CRISPR/Cas9 has fundamentally changed the ease and speed of genome editing in many organisms. In eukaryotes, the CRISPR/Cas9 system utilizes a "guide" RNA to enable the Cas9 nuclease to make a double-strand break at a particular genome locus, which is repaired by non-homologous end joining (NHEJ) repair enzymes, often generating random mutations in the process. A specific alteration of the target genome can also be generated by supplying a DNA template in vivo with a desired mutation, which is incorporated by homology-directed repair. However, E. coli lacks robust systems for double-strand break repair. Thus, in contrast to eukaryotes, targeting E. coli chromosomal DNA with Cas9 causes cell death. However, Cas9-mediated killing of bacteria can be exploited to select against cells with a specified genotype within a mixed population. In combination with the well described λ-Red system for recombination in E. coli, we created a highly efficient system for marker-free and scarless genome editing. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  10. Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7.

    Science.gov (United States)

    Cooper, Kerry K; Mandrell, Robert E; Louie, Jacqueline W; Korlach, Jonas; Clark, Tyson A; Parker, Craig T; Huynh, Steven; Chain, Patrick S; Ahmed, Sanaa; Carter, Michelle Qiu

    2014-01-10

    Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no complete genomes for O145 in public databases. We determined the complete genome sequences of two O145 strains (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a Belgium ice-cream-associated outbreak (RM13516). Both strains contain one chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514 and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes revealed a large core (5,173 genes) and a considerable amount of strain-specific genes. Additionally, the two EcO145 genomes display distinct chromosomal architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and methylation profile (methylome). Comparative analysis of EcO145 genomes to other completely sequenced STEC and other E. coli and Shigella genomes revealed that, unlike any other known non-O157 EHEC strain, EcO145 ascended from a common lineage with EcO157/EcO55. This evolutionary relationship was further supported by the pangenome analysis of the 10 EHEC str ains. Of the 4,192 EHEC core genes, EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC strains. Our data provide evidence that EcO145 and EcO157 evolved from a common lineage, but ultimately each serotype evolves via a lineage-independent nature to EHEC by acquisition of the core set of EHEC virulence factors, including the genes encoding Shiga toxin and the large virulence plasmid. The large variation between the two EcO145 genomes suggests a distinctive

  11. Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.

    Science.gov (United States)

    Chen, Huiyi; Shiroguchi, Katsuyuki; Ge, Hao; Xie, Xiaoliang Sunney

    2015-01-12

    An essential part of gene expression is the coordination of RNA synthesis and degradation, which occurs in the same cellular compartment in bacteria. Here, we report a genome-wide RNA degradation study in Escherichia coli using RNA-seq, and present evidence that the stereotypical exponential RNA decay curve obtained using initiation inhibitor, rifampicin, consists of two phases: residual RNA synthesis, a delay in the interruption of steady state that is dependent on distance relative to the mRNA's 5' end, and the exponential decay. This gives a more accurate RNA lifetime and RNA polymerase elongation rate simultaneously genome-wide. Transcripts typically have a single RNA decay constant along all positions, which is distinct between different operons, indicating that RNA stability is unlikely determined by local sequences. These measurements allowed us to establish a model for RNA processing involving co-transcriptional degradation, providing quantitative description of the macromolecular coordination in gene expression in bacteria on a system-wide level. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.

  12. Comparative genome analysis of a thermotolerant Escherichia coli obtained by Genome Replication Engineering Assisted Continuous Evolution (GREACE) and its parent strain provides new understanding of microbial heat tolerance.

    Science.gov (United States)

    Luan, Guodong; Bao, Guanhui; Lin, Zhao; Li, Yang; Chen, Zugen; Li, Yin; Cai, Zhen

    2015-12-25

    Heat tolerance of microbes is of great importance for efficient biorefinery and bioconversion. However, engineering and understanding of microbial heat tolerance are difficult and insufficient because it is a complex physiological trait which probably correlates with all gene functions, genetic regulations, and cellular metabolisms and activities. In this work, a novel strain engineering approach named Genome Replication Engineering Assisted Continuous Evolution (GREACE) was employed to improve the heat tolerance of Escherichia coli. When the E. coli strain carrying a mutator was cultivated under gradually increasing temperature, genome-wide mutations were continuously generated during genome replication and the mutated strains with improved thermotolerance were autonomously selected. A thermotolerant strain HR50 capable of growing at 50°C on LB agar plate was obtained within two months, demonstrating the efficiency of GREACE in improving such a complex physiological trait. To understand the improved heat tolerance, genomes of HR50 and its wildtype strain DH5α were sequenced. Evenly distributed 361 mutations covering all mutation types were found in HR50. Closed material transportations, loose genome conformation, and possibly altered cell wall structure and transcription pattern were the main differences of HR50 compared with DH5α, which were speculated to be responsible for the improved heat tolerance. This work not only expanding our understanding of microbial heat tolerance, but also emphasizing that the in vivo continuous genome mutagenesis method, GREACE, is efficient in improving microbial complex physiological trait. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. [Study on an inquiry-based teaching case in genomics curriculum: identifying virulence factors of Escherichia coli by using comparative genomics].

    Science.gov (United States)

    Jidong, Zhou; Yudong, Li

    2015-02-01

    Genomics is the core subject of various "omics" and it also becomes a topic of increasing interest in undergraduate curricula of biological sciences. However, the study on teaching methodology of genomics courses was very limited so far. Here we report an application of inquiry-based teaching in genomics courses by using virulence factors of Escherichia coli as an example of comparative genomics study. Specially, students first built a multiple-genome alignment of different E. coli strains to investigate the gene conservation using the Mauve tool; then putative virulence factor genes were identified by using BLAST tool to obtain gene annotations. The teaching process was divided into five modules: situation, resources, task, process and evaluation. Learning-assessment results revealed that students had acquired the knowledge and skills of genomics, and their learning interest and ability of self-study were also motivated. Moreover, the special teaching case can be applied to other related courses, such as microbiology, bioinformatics, molecular biology and food safety detection technology.

  14. K-12 students with concussions: a legal perspective.

    Science.gov (United States)

    Zirkel, Perry A; Brown, Brenda Eagan

    2015-04-01

    This article provides a multipart analysis of the public schools' responsibility for students with concussions. The first part provides the prevailing diagnostic definitions of concussions and postconcussive syndrome. The second and central part provides (a) the legal framework of the two overlapping federal laws--the Individuals with Disabilities Education Act and Section 504 of the Rehabilitation Act and the varying state laws or local policies for individual health plans and (b) a summary of the developing body of hearing officer decisions, court decisions, and Office for Civil Rights rulings that have applied this framework to K-12 students with concussions. The final part offers recommendations for proactive return to school policies, with the school nurse playing a central supporting role. © The Author(s) 2014.

  15. How to Get Successfully Involved with K-12 Education

    Science.gov (United States)

    Duncan, D.; Fraknoi, A.; Bennett, M.

    1998-05-01

    Many astronomers now have some involvement in K-12 education, either through their children, through large projects with an education or outreach office, or through an educational component to their own grants. Some may need to incorporate education components into future proposals. For those new to education, it can be difficult to decide how best to use their limited resources without "re-inventing the wheel." Some astronomers are comfortable taking a direct role in the classroom or working with teachers, others prefer developing web-based or printed materials, while still others wouldrather work with local schools of education to enhance the training of future teachers. Which of these roles is most useful? In this session, participants will learn what has worked well in the past, with special attention paid to ways in which astronomers' and physicists' training and instincts may fail them when working in education. Invited teachers will describe their classrooms and how astronomers can be most helpful to them. Sample (successful) activities will be demonstrated, and information given about the wide range of existing astronomy and space-science education programs around the country. A full menu of useful ways that astronomers can get involved will be presented, as well as the organizations and institutions which can help in devising a meaningful education program. Handouts will include a catalog of national astronomy education projects, a list of educational web sites, information about the NASA OSS education brokers and facilitators, examples of successful educational materials, and a listing of roles astronomers have played or could play to enhance K-12 education. Registration is required; see the AAS Education WWW page or email aased@aas.org.

  16. The Aloha Telescope for K-12 STEM Education

    Science.gov (United States)

    Sowell, James R.

    2015-01-01

    How does one bring night-time astronomical observations into the classroom? How does a teacher - during the school day - show students the craters on the Moon, the rings of Saturn, or the four Galilean moons of Jupiter? One of the greatest drawbacks to teaching Astronomy is the lack of real-time telescopic observations during the school day, and yet this is a very exciting time for astronomical discoveries. The solution is to access a telescope in a substantially different time zone where it is still night. This facility - the Aloha Telescope - on Maui has already been established by a partnership between Georgia Tech and the Air Force Research Lab. This robotic telescope's sole purpose is for K-12 education, as it is equipped with a video-camera and is operated remotely via high-speed internet connections. This facility and its outreach program allow east-coast teachers and, in turn, students to have local daytime access to - and direct control of - the telescope. When observing the Moon, teachers and students will move the telescope wherever they wish across the highly-magnified lunar surface (~ 5 arcminute FOV). This telescope will enable night-time astronomical observations to come alive as day-time activities and will be an important tool for STEM education and activities. The use of the Aloha Telescope requires minimal training and is free after registering for a date and time.Dr. Sowell has written specific telescopic exercises and surface feature tours appropriate for K-12 and college-level users. These exercises, and other aspects of the Aloha Telescope and program, are posted on the website at http://aloha.gatech.edu

  17. Genomics of Escherichia and Shigella

    Science.gov (United States)

    Perna, Nicole T.

    The laboratory workhorse Escherichia coli K-12 is among the most intensively studied living organisms on earth, and this single strain serves as the model system behind much of our understanding of prokaryotic molecular biology. Dense genome sequencing and recent insightful comparative analyses are making the species E. coli, as a whole, an emerging system for studying prokaryotic population genetics and the relationship between system-scale, or genome-scale, molecular evolution and complex traits like host range and pathogenic potential. Genomic perspective has revealed a coherent but dynamic species united by intraspecific gene flow via homologous lateral or horizontal transfer and differentiated by content flux mediated by acquisition of DNA segments from interspecies transfers.

  18. Genome reannotation of Escherichia coli CFT073 with new insights into virulence

    Directory of Open Access Journals (Sweden)

    Hu Gang-Qing

    2009-11-01

    Full Text Available Abstract Background As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence. We carried out a systematic reannotation by combining automated annotation tools with manual efforts to provide a comprehensive understanding of virulence for the CFT073 genome. Results The reannotation excluded 608 coding sequences from the RefSeq annotation. Meanwhile, a total of 299 coding sequences were newly added, about one third of them are found in genomic island (GI regions while more than one fifth of them are located in virulence related regions pathogenicity islands (PAIs. Furthermore, there are totally 341 genes were relocated with their translational initiation sites (TISs, which resulted in a high quality of gene start annotation. In addition, 94 pseudogenes annotated in RefSeq were thoroughly inspected and updated. The number of miscellaneous genes (sRNAs has been updated from 6 in RefSeq to 46 in the reannotation. Based on the adjustment in the reannotation, subsequent analysis were conducted by both general and case studies on new virulence factors or new virulence-associated genes that are crucial during the urinary tract infections (UTIs process, including invasion, colonization, nutrition uptaking and population density control. Furthermore, miscellaneous RNAs collected in the reannotation are believed to contribute to the virulence of strain CFT073. The reannotation including the nucleotide data, the original RefSeq annotation, and all reannotated results is freely available via http://mech.ctb.pku.edu.cn/CFT073/. Conclusion As a result, the reannotation presents a more comprehensive picture of mechanisms of uropathogenicity of UPEC strain CFT073

  19. In vivo Assembly in Escherichia coli of Transformation Vectors for Plastid Genome Engineering.

    Science.gov (United States)

    Wu, Yuyong; You, Lili; Li, Shengchun; Ma, Meiqi; Wu, Mengting; Ma, Lixin; Bock, Ralph; Chang, Ling; Zhang, Jiang

    2017-01-01

    Plastid transformation for the expression of recombinant proteins and entire metabolic pathways has become a promising tool for plant biotechnology. However, large-scale application of this technology has been hindered by some technical bottlenecks, including lack of routine transformation protocols for agronomically important crop plants like rice or maize. Currently, there are no standard or commercial plastid transformation vectors available for the scientific community. Construction of a plastid transformation vector usually requires tedious and time-consuming cloning steps. In this study, we describe the adoption of an in vivo Escherichia coli cloning (iVEC) technology to quickly assemble a plastid transformation vector. The method enables simple and seamless build-up of a complete plastid transformation vector from five DNA fragments in a single step. The vector assembled for demonstration purposes contains an enhanced green fluorescent protein (GFP) expression cassette, in which the gfp transgene is driven by the tobacco plastid ribosomal RNA operon promoter fused to the 5' untranslated region (UTR) from gene10 of bacteriophage T7 and the transcript-stabilizing 3'UTR from the E. coli ribosomal RNA operon rrnB. Successful transformation of the tobacco plastid genome was verified by Southern blot analysis and seed assays. High-level expression of the GFP reporter in the transplastomic plants was visualized by confocal microscopy and Coomassie staining, and GFP accumulation was ~9% of the total soluble protein. The iVEC method represents a simple and efficient approach for construction of plastid transformation vector, and offers great potential for the assembly of increasingly complex vectors for synthetic biology applications in plastids.

  20. In vivo Assembly in Escherichia coli of Transformation Vectors for Plastid Genome Engineering

    Directory of Open Access Journals (Sweden)

    Yuyong Wu

    2017-08-01

    Full Text Available Plastid transformation for the expression of recombinant proteins and entire metabolic pathways has become a promising tool for plant biotechnology. However, large-scale application of this technology has been hindered by some technical bottlenecks, including lack of routine transformation protocols for agronomically important crop plants like rice or maize. Currently, there are no standard or commercial plastid transformation vectors available for the scientific community. Construction of a plastid transformation vector usually requires tedious and time-consuming cloning steps. In this study, we describe the adoption of an in vivo Escherichia coli cloning (iVEC technology to quickly assemble a plastid transformation vector. The method enables simple and seamless build-up of a complete plastid transformation vector from five DNA fragments in a single step. The vector assembled for demonstration purposes contains an enhanced green fluorescent protein (GFP expression cassette, in which the gfp transgene is driven by the tobacco plastid ribosomal RNA operon promoter fused to the 5′ untranslated region (UTR from gene10 of bacteriophage T7 and the transcript-stabilizing 3′UTR from the E. coli ribosomal RNA operon rrnB. Successful transformation of the tobacco plastid genome was verified by Southern blot analysis and seed assays. High-level expression of the GFP reporter in the transplastomic plants was visualized by confocal microscopy and Coomassie staining, and GFP accumulation was ~9% of the total soluble protein. The iVEC method represents a simple and efficient approach for construction of plastid transformation vector, and offers great potential for the assembly of increasingly complex vectors for synthetic biology applications in plastids.

  1. Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

    Directory of Open Access Journals (Sweden)

    LeClerc Joseph E

    2011-07-01

    Full Text Available Abstract Background The gene content of a diverse group of 183 unique Escherichia coli and Shigella isolates was determined using the Affymetrix GeneChip® E. coli Genome 2.0 Array, originally designed for transcriptome analysis, as a genotyping tool. The probe set design utilized by this array provided the opportunity to determine the gene content of each strain very accurately and reliably. This array constitutes 10,112 independent genes representing four individual E. coli genomes, therefore providing the ability to survey genes of several different pathogen types. The entire ECOR collection, 80 EHEC-like isolates, and a diverse set of isolates from our FDA strain repository were included in our analysis. Results From this study we were able to define sets of genes that correspond to, and therefore define, the EHEC pathogen type. Furthermore, our sampling of 63 unique strains of O157:H7 showed the ability of this array to discriminate between closely related strains. We found that individual strains of O157:H7 differed, on average, by 197 probe sets. Finally, we describe an analysis method that utilizes the power of the probe sets to determine accurately the presence/absence of each gene represented on this array. Conclusions These elements provide insights into understanding the microbial diversity that exists within extant E. coli populations. Moreover, these data demonstrate that this novel microarray-based analysis is a powerful tool in the field of molecular epidemiology and the newly emerging field of microbial forensics.

  2. SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs.

    Science.gov (United States)

    Zautner, Andreas E; Goldschmidt, Anne-Marie; Thürmer, Andrea; Schuldes, Jörg; Bader, Oliver; Lugert, Raimond; Groß, Uwe; Stingl, Kerstin; Salinas, Gabriela; Lingner, Thomas

    2015-12-21

    Campylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates significant differences in DNA methylation between both microbial species. The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C. jejuni and Helicobacter pylori. Using one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %. Only five dominant methylation motifs have been identified in C. jejuni, which have been associated with known RM-systems. C. coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP, methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP RM-system has been described for H. pylori. The remaining methylation motifs are specific for C. coli BfR-CA-9557 and have been neither detected

  3. Barriers in the Physics Pipeline from K-12 to Tenure

    Science.gov (United States)

    Kilburn, Micha

    2016-09-01

    The lack of diversity in physics is a known problem, and yet efforts to change our demographics have only had minor effects during the last decade. I will explain some of the hidden barriers that dissuade underrepresented minorities in becoming physicists using a framework borrowed from sociology, Maslow's hierarchy of needs. I will draw from current research at the undergraduate to faculty levels over a variety of STEM fields that are also addressing a lack of diversity. I will also provide analysis from the Joint Institute for Nuclear Astrophysics Center for the Evolution of Elements (JINA-CEE) outreach programs to understand the likelihood of current K-12 students in becoming physicists. Specifically, I will present results from the pre-surveys from our Art 2 Science Camps (ages 8-14) about their attitudes towards science as well as results from analysis of teacher recommendations for our high school summer program. I will conclude with a positive outlook describing the pipeline created by JINA-CEE to retain students from middle school through college. This work was supported in part by the National Science Foundation under Grant No. PHY-1430152 (JINA Center for the Evolution of the Elements).

  4. "Flipping" educational technology professional development for K-12 educators

    Science.gov (United States)

    Spencer, Daniel

    As the demand for more effective professional development increases in K-12 schools, trainers must adjust their training methods to meet the needs of their teacher learners. Just as lecture-heavy, teacher-centered instruction only meet the learning needs of a small minority of students, "sit and get" professional development rarely results in the teachers gaining the skills and confidence necessary to use technology effectively in their instruction. To resolve the frustrations of teachers related to ineffective professional development, a "Flipped PD" training model was developed based on the learning needs of adult learners, the integration of technological, pedagogical, and content knowledge (TPACK), learning activities, and the Flipped Classroom concept. Under this model, training shifts from a passive, trainer-centered format, to an active, learner-centered format where teachers learn to use technology in their classrooms by first focusing on pedagogical issues, then choosing the options that work best for addressing those issues in their unique situation, and completing "learn-by-doing" projects. Those who participate in "Flipped PD" style trainings tend to have more confidence upon completion that they can use the tools they were trained on in their teaching, as well as believe that the PD was engaging and a good use of their time.

  5. Students with Special Health Care Needs in K-12 Virtual Schools

    National Research Council Canada - National Science Library

    Heidi Fernandez; Richard E Ferdig; Lindsay A Thompson; Katherine Schottke; Erik W Black

    2016-01-01

      This study sought to establish a baseline for understanding the epidemiology of online K-12 students with special health care needs, determine the prevalence in K-12 online schooling of students...

  6. Urinary tract infection drives genome instability in uropathogenic Escherichia coli and necessitates translesion synthesis DNA polymerase IV for virulence.

    Science.gov (United States)

    Gawel, Damian; Seed, Patrick C

    2011-01-01

    Uropathogenic Escherichia coli (UPEC) produces ~80% of community-acquired UTI, the second most common infection in humans. During UTI, UPEC has a complex life cycle, replicating and persisting in intracellular and extracellular niches. Host and environmental stresses may affect the integrity of the UPEC genome and threaten its viability. We determined how the host inflammatory response during UTI drives UPEC genome instability and evaluated the role of multiple factors of genome replication and repair for their roles in the maintenance of genome integrity and thus virulence during UTI. The urinary tract environment enhanced the mutation frequency of UPEC ~100-fold relative to in vitro levels. Abrogation of inflammation through a host TLR4-signaling defect significantly reduced the mutation frequency, demonstrating in the importance of the host response as a driver of UPEC genome instability. Inflammation induces the bacterial SOS response, leading to the hypothesis that the UPEC SOS-inducible translesion synthesis (TLS) DNA polymerases would be key factors in UPEC genome instability during UTI. However, while the TLS DNA polymerases enhanced in vitro, they did not increase in vivo mutagenesis. Although it is not a source of enhanced mutagenesis in vivo, the TLS DNA polymerase IV was critical for the survival of UPEC during UTI during an active inflammatory assault. Overall, this study provides the first evidence of a TLS DNA polymerase being critical for UPEC survival during urinary tract infection and points to independent mechanisms for genome instability and the maintenance of genome replication of UPEC under host inflammatory stress.

  7. Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls

    DEFF Research Database (Denmark)

    Nielsen, Karen Leth; Stegger, Marc; Kiil, Kristoffer

    2017-01-01

    -only isolates, respectively. Comparison of the accessory genome of UTI isolates to faecal isolates revealed 35 gene families which were significantly more prevalent in the UTI isolates compared to the faecal isolates, although none of these were unique to one of the two groups. Of these 35, 22 belonged...... to a genomic island and three putatively belonged to a type VI secretion system (T6SS). MLST types and SNP phylogeny indicated no clustering of the UTI or faecal E. coli from patients distinct from the control faecal isolates, although there was an overrepresentation of UTI isolates belonging to clonal...

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

    Science.gov (United States)

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

    2011-04-26

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

  9. Whole-Genome Sequences of the Archetypal K1 Escherichia coli Neonatal Isolate RS218 and Contemporary Neonatal Bacteremia Clinical Isolates SCB11, SCB12, and SCB15

    OpenAIRE

    Day, Michael W.; Jackson, Lydgia A.; Akins, Darrin R.; Dyer, David W.; Chavez-Bueno, Susana

    2015-01-01

    Neonatal bacteremia Escherichia?coli strains commonly belong to the K1 capsular type. Their ability to cause invasive neonatal disease appears to be determined by other virulence factors that have yet to be identified. We report here the genome sequences of four E.?coli neonatal bacteremia isolates, including that of the archetypal strain RS218.

  10. Complete Draft Genome Sequence of Escherichia coli KRX, a Strain for Efficient Cloning and High-Yield Expression of Proteins under Control of the T7 RNA Polymerase

    OpenAIRE

    Schwarzhans, Jan-Philipp; Wibberg, Daniel; Winkler, Anika; Kalinowski, Jörn; Friehs, Karl

    2017-01-01

    ABSTRACT Escherichia coli KRX is a strain offering both a high transformation efficiency and the possibility to produce the target protein to high yields in one host, avoiding additional cloning steps. Here, the draft genome sequence of E. coli KRX is presented and provides the genetic basis for additional biotechnological applications.

  11. High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

    DEFF Research Database (Denmark)

    Kokotovic, Branko; On, Stephen L.W.

    1999-01-01

    A method for high-resolution genomic fingerprinting of the enteric pathogens Campylobacter jejuni and Campylobacter coli, based on the determination of amplified fragment length polymorphism, is described. The potential of this method for molecular epidemiological studies of these species...... to available epidemiological data. We conclude that this amplified fragment length polymorphism fingerprinting method may be a highly effective tool for molecular epidemiological studies of Campylobacter spp....

  12. Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains

    Science.gov (United States)

    Shiga toxin-producing Escherichia coli (STEC) O26 is the second leading E. coli serogroup responsible for human illness outbreaks behind E. coli O157:H7. Recent outbreaks have been linked to emerging pathogenic O26:H11 strains harboring stx2 only. Cattle have been recognized as an important reserv...

  13. Cloning the simian varicella virus genome in E. coli as an infectious bacterial artificial chromosome.

    Science.gov (United States)

    Gray, Wayne L; Zhou, Fuchun; Noffke, Juliane; Tischer, B Karsten

    2011-05-01

    Simian varicella virus (SVV) is closely related to human varicella-zoster virus and causes varicella and zoster-like disease in nonhuman primates. In this study, a mini-F replicon was inserted into a SVV cosmid, and infectious SVV was generated by co-transfection of Vero cells with overlapping SVV cosmids. The entire SVV genome, cloned as a bacterial artificial chromosome (BAC), was stably propagated upon serial passage in E. coli. Transfection of pSVV-BAC DNA into Vero cells yielded infectious SVV (rSVV-BAC). The mini-F vector sequences flanked by loxP sites were removed by co-infection of Vero cells with rSVV-BAC and adenovirus expressing Cre-recombinase. Recombinant SVV generated using the SVV-BAC genetic system has similar molecular and in vitro replication properties as wild-type SVV. To demonstrate the utility of this approach, a SVV ORF 10 deletion mutant was created using two-step Red-mediated recombination. The results indicate that SVV ORF 10, which encodes a homolog of the HSV-1 virion VP-16 transactivator protein, is not essential for in vitro replication but is required for optimal replication in cell culture.

  14. Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.

    Science.gov (United States)

    Hacker, William C; Li, Shuxiang; Elcock, Adrian H

    2017-07-27

    We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of 'fractal globules,' and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Investigating the Potential of MOOCs in K-12 Teaching and Learning Environments

    Science.gov (United States)

    Nigh, Jennifer; Pytash, Kristine E.; Ferdig, Richard E.; Merchant, William

    2015-01-01

    The massive open online course (MOOC) is a relatively new concept in K-12 teaching and learning environments. Although significant work has been done with MOOCs since 2008, it has only been recently that MOOCs have been studied with K-12 populations. The purpose of this study was to further examine the motivation of K-12 students enrolled in a…

  16. K-12 Education Nonprofit Employees' Perceptions of Strategies for Recruiting and Retaining Employees

    Science.gov (United States)

    Byrne, Tara Marie

    2013-01-01

    This qualitative study explored the key reasons individuals who work in K-12 education nonprofit organizations enter the field of K-12 nonprofit education and their motivations for doing so. The purpose of this study was to find new strategies for recruiting and retaining K-12 education nonprofit employees by examining the obstacles that exist to…

  17. Interview with Joe Freidhoff: A Bird's-Eye View of K-12 Online Learning

    Science.gov (United States)

    Pourreau, Leslie

    2015-01-01

    The intent of this article is to introduce long-time "Online Learning" readership to the field of K-12 online learning while also providing direction for the K-12 online learning scholars about where the field is going or should be going in terms of meeting the needs of K-12 stakeholders. Recently an interview was conducted with Dr. Joe…

  18. K-12 Teachers Encounter Digital Games: A Qualitative Investigation of Teachers' Perceptions of the Potential of Digital Games for K-12 Education

    Science.gov (United States)

    Dickey, Michele D.

    2015-01-01

    The purpose of this study is to investigate teachers' perceptions of the integration of digital games for K-12 education. Specifically, this qualitative investigation focuses on reflective dialogued gathered from a group of K-12 educators about their experiences and perceptions of learning about and playing digital games for teaching and learning.…

  19. K-12 Phenology Lessons for the Phenocam Project

    Science.gov (United States)

    Bennett, K. F.

    2013-12-01

    Phenology is defined as periodic [or annual] life cycles of plants and animals driven by seasonal environmental changes. Climate change impinges a strong effect on phenology, potentially altering the structure and functioning of ecosystems. In the fall of 2011, the Ashburnham-Westminster Regional School District became the first of five schools to join Harvard University's Phenocam Network with the installation of a webcam to monitor phenology (or 'phenocam') at Overlook Middle School in Ashburnham, Massachusetts. Our school district is now part of a network of near-surface remote sensing phenocams that capture and send images of forest, shrub, and grassland vegetation cover at more than 130 diverse sites in North America. Our phenocam provides a digital image every half hour of the mixed forest canopy north from the school, enabling the detection of changes in canopy development, quantified as canopy 'greenness'. As a part of the Phenocam project, students at the K-12 level have expanded the scope of phenological monitoring protocol that is part of the Harvard Forest Schoolyard Ecology Program, Buds, Leaves, and Global Warming. In this protocol, students work with ecologists at Harvard Forest to monitor buds and leaves on schoolyard trees to determine the length of the growing season, giving them the opportunity to be a part of real and important research concerning the critical environmental issue of climate change. Students involved in the Buds, Leaves, and Global Warming study have the opportunity to compare their ground data on budburst, color change, and leaf drop to the phenocam images, as well as to similar forested sites in locations throughout the United States. Lessons have been developed for comparing student data to phenocam images, canopy greenness time series graphs extracted from the images, and satellite data. Lessons addressing map scale and the Urban Heat Island effect will also be available for teachers. This project will greatly enhance the

  20. Genome-Wide Discovery of Genes Required for Capsule Production by Uropathogenic Escherichia coli.

    Science.gov (United States)

    Goh, Kelvin G K; Phan, Minh-Duy; Forde, Brian M; Chong, Teik Min; Yin, Wai-Fong; Chan, Kok-Gan; Ulett, Glen C; Sweet, Matthew J; Beatson, Scott A; Schembri, Mark A

    2017-10-24

    Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract and bloodstream infections and possesses an array of virulence factors for colonization, survival, and persistence. One such factor is the polysaccharide K capsule. Among the different K capsule types, the K1 serotype is strongly associated with UPEC infection. In this study, we completely sequenced the K1 UPEC urosepsis strain PA45B and employed a novel combination of a lytic K1 capsule-specific phage, saturated Tn5 transposon mutagenesis, and high-throughput transposon-directed insertion site sequencing (TraDIS) to identify the complement of genes required for capsule production. Our analysis identified known genes involved in capsule biosynthesis, as well as two additional regulatory genes (mprA and lrhA) that we characterized at the molecular level. Mutation of mprA resulted in protection against K1 phage-mediated killing, a phenotype restored by complementation. We also identified a significantly increased unidirectional Tn5 insertion frequency upstream of the lrhA gene and showed that strong expression of LrhA induced by a constitutive Pcl promoter led to loss of capsule production. Further analysis revealed loss of MprA or overexpression of LrhA affected the transcription of capsule biosynthesis genes in PA45B and increased sensitivity to killing in whole blood. Similar phenotypes were also observed in UPEC strains UTI89 (K1) and CFT073 (K2), demonstrating that the effects were neither strain nor capsule type specific. Overall, this study defined the genome of a UPEC urosepsis isolate and identified and characterized two new regulatory factors that affect UPEC capsule production.IMPORTANCE Urinary tract infections (UTIs) are among the most common bacterial infections in humans and are primarily caused by uropathogenic Escherichia coli (UPEC). Many UPEC strains express a polysaccharide K capsule that provides protection against host innate immune factors and contributes to survival and

  1. Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli.

    Science.gov (United States)

    Englaender, Jacob A; Jones, J Andrew; Cress, Brady F; Kuhlman, Thomas E; Linhardt, Robert J; Koffas, Mattheos A G

    2017-04-21

    Chromosomal integration offers a selection-free alternative to DNA plasmids for expression of foreign proteins and metabolic pathways. Episomal plasmid DNA is convenient but has drawbacks including increased metabolic burden and the requirement for selection in the form of antibiotics. E. coli has long been used for the expression of foreign proteins and for the production of valuable metabolites by expression of complete metabolic pathways. The gene encoding the fluorescent reporter protein mCherry was integrated into four genomic loci on the E. coli chromosome to measure protein expression at each site. Expression levels ranged from 25% to 500% compared to the gene expressed on a high-copy plasmid. Modular expression of DNA is one of the most commonly used methods for optimizing metabolite production by metabolic engineering. By combining a recently developed method for integration of large synthetic DNA constructs into the genome, we were able to integrate two foreign pathways into the same four genomic loci. We have demonstrated that only one of the genomic loci resulted in the production of violacein, and that all four loci produced trans-cinnamic acid from the TAL pathway.

  2. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.

    Science.gov (United States)

    Musicha, Patrick; Feasey, Nicholas A; Cain, Amy K; Kallonen, Teemu; Chaguza, Chrispin; Peno, Chikondi; Khonga, Margaret; Thompson, Sarah; Gray, Katherine J; Mather, Alison E; Heyderman, Robert S; Everett, Dean B; Thomson, Nicholas R; Msefula, Chisomo L

    2017-06-01

    Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.

  3. Regulatory mutants of the aroF-tyrA operon of Escherichia coli K-12.

    Science.gov (United States)

    Cobbett, C S; Delbridge, M L

    1987-06-01

    The regulatory region of the aroF-tyrA operon was fused to the chloramphenicol acetyltransferase (cat) gene on a plasmid vector. Expression of the cat gene was subject to repression by tyrR+. This fusion was used to isolate regulatory mutants with increased expression of the cat gene in which repression by tyrR+ was affected. Nucleotide sequencing of these mutants has led to the identification of three sites involved in the repression of aroF by tyrR+. The existence of a functional promoter divergently transcribing from the aroF regulatory region was also demonstrated by using the cat fusion vector. The expression of this promoter is also regulated by tyrR+.

  4. Cool Science: K-12 Climate Change Art Displayed on Buses

    Science.gov (United States)

    Chen, R. F.; Lustick, D. S.; Lohmeier, J.; Thompson, S. R.

    2015-12-01

    Cool science is an art contest where K12 students create placards (7" x 22") to educate the public about climate change. Students are prompted to create their artwork in response to questions such as: What is the evidence for climate change? How does climate change impact your local community? What can you do to reduce the impacts of climate change? In each of three years, 500-600 student entrees have been submitted from more than 12 school districts across Massachusetts. A panel of judges including scientists, artists, rapid transit representatives, and educators chooses elementary, middle, and high school winners. Winners (6), runners-up (6), and honorable mentions (12) and their families and teachers are invited to an annual Cool Science Award Ceremony to be recognized and view winning artwork. All winning artwork is posted on the Cool Science website. The winning artwork (2 per grade band) is converted into placards (11" x 28") and posters (2.5' x 12') that are placed on the inside (placards) and outside (posters) of buses. Posters are displayed for one month. So far, Cool Science was implemented in Lowell, MA where over 5000 public viewers see the posters daily on the sides of Lowell Rapid Transit Authority (LRTA) buses, making approximately 1,000,000 impressions per year. Cool Science acts to increase climate literacy in children as well as the public, and as such promotes intergenerational learning. Using art in conjunction with science learning about climate change appears to be effective at engaging not just traditionally high achieving science students, but also those interested in the creative arts. Hearing winners' stories about how they created their artwork and what this contest meant to them supports the idea that Cool Science attracts a wide diversity of students. Parents discuss climate change with their children. Multiple press releases announcing the winners further promotes the awareness of climate change throughout school districts and their

  5. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

    DEFF Research Database (Denmark)

    Monk, Jonathan M; Koza, Anna; Campodonico, Miguel A

    2016-01-01

    Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology......, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics, and genome-scale modeling. Metabolic physiology and gene expression varied...... widely with downstream implications for productivity, product yield, and titer. These differences could be linked to differential regulatory structure. Analyzing high-flux reactions and expression of encoding genes resulted in a correlated and quantitative link between these sets, with strain...

  6. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.

    Science.gov (United States)

    Fang, Gang; Munera, Diana; Friedman, David I; Mandlik, Anjali; Chao, Michael C; Banerjee, Onureena; Feng, Zhixing; Losic, Bojan; Mahajan, Milind C; Jabado, Omar J; Deikus, Gintaras; Clark, Tyson A; Luong, Khai; Murray, Iain A; Davis, Brigid M; Keren-Paz, Alona; Chess, Andrew; Roberts, Richard J; Korlach, Jonas; Turner, Steve W; Kumar, Vipin; Waldor, Matthew K; Schadt, Eric E

    2012-12-01

    Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical modifications such as methylation but has not previously been applied on a genome-wide scale. We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407 putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli strain. We obtained strand-specific information for methylation sites and a quantitative assessment of the frequency of methylation at each modified position. We deduced the sequence motifs recognized by the methyltransferase enzymes present in this strain without prior knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded methyltransferase-endonuclease (restriction-modification; RM) system induced global transcriptional changes and led to gene amplification, suggesting that the role of RM systems extends beyond protecting host genomes from foreign DNA.

  7. Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing

    Directory of Open Access Journals (Sweden)

    Philip M. Ashton

    2015-02-01

    Full Text Available The ability of Shiga toxin-producing Escherichia coli (STEC to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx subtype. Given the link between Stx2a subtype and disease severity, we sought to identify the stx subtypes present in whole genome sequences (WGS of 444 isolates of STEC O157. Difficulties in assembling the stx genes in some strains were overcome by using two complementary bioinformatics methods: mapping and de novo assembly. We compared the WGS analysis with the results obtained using a PCR approach and investigated the diversity within and between the subtypes. All strains of STEC O157 in this study had stx1a, stx2a or stx2c or a combination of these three genes. There was over 99% (442/444 concordance between PCR and WGS. When common source strains were excluded, 236/349 strains of STEC O157 had multiple copies of different Stx subtypes and 54 had multiple copies of the same Stx subtype. Of those strains harbouring multiple copies of the same Stx subtype, 33 had variants between the alleles while 21 had identical copies. Strains harbouring Stx2a only were most commonly found to have multiple alleles of the same subtype (42%. Both the PCR and WGS approach to stx subtyping provided a good level of sensitivity and specificity. In addition, the WGS data also showed there were a significant proportion of strains harbouring multiple alleles of the same Stx subtype associated with clinical disease in England.

  8. Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli

    Directory of Open Access Journals (Sweden)

    Lapointe François-Joseph

    2011-07-01

    Full Text Available Abstract Background We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL approaches. Results We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study, and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements. Conclusions Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc., forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to

  9. Comparative Genomic Analysis of Escherichia coli O157:H7 Isolated from Super-Shedder and Low-Shedder Cattle

    Science.gov (United States)

    Munns, Krysty D.; Zaheer, Rahat; Xu, Yong; Stanford, Kim; Laing, Chad R.; Gannon, Victor P. J.; Selinger, L. Brent; McAllister, Tim A.

    2016-01-01

    Cattle are the primary reservoir of the foodborne pathogen Escherichia coli O157:H7, with the concentration and frequency of E. coli O157:H7 shedding varying substantially among individual hosts. The term ‘‘super-shedder” has been applied to cattle that shed ≥104 cfu E. coli O157:H7/g of feces. Super-shedders have been reported to be responsible for the majority of E. coli O157:H7 shed into the environment. The objective of this study was to determine if there are phenotypic and/or genotypic differences between E. coli O157:H7 isolates obtained from super-shedder compared to low-shedder cattle. From a total of 784 isolates, four were selected from low-shedder steers and six isolates from super-shedder steers (4.01–8.45 log cfu/g feces) for whole genome sequencing. Isolates were phage and clade typed, screened for substrate utilization, pH sensitivity, virulence gene profiles and Stx bacteriophage insertion (SBI) sites. A range of 89–2473 total single nucleotide polymorphisms (SNPs) were identified when sequenced strains were compared to E. coli O157:H7 strain Sakai. More non-synonymous SNP mutations were observed in low-shedder isolates. Pan-genomic and SNPs comparisons did not identify genetic segregation between super-shedder or low-shedder isolates. All super-shedder isolates and 3 of 4 of low-shedder isolates were typed as phage type 14a, SBI cluster 3 and SNP clade 2. Super-shedder isolates displayed increased utilization of galactitol, thymidine and 3-O-β-D-galactopyranosyl-D-arabinose when compared to low-shedder isolates, but no differences in SNPs were observed in genes encoding for proteins involved in the metabolism of these substrates. While genetic traits specific to super-shedder isolates were not identified in this study, differences in the level of gene expression or genes of unknown function may still contribute to some strains of E. coli O157:H7 reaching high densities within bovine feces. PMID:27018858

  10. iML1515, a knowledgebase that computes Escherichia coli traits

    DEFF Research Database (Denmark)

    Monk, Jonathan M.; Lloyd, Colton J.; Brunk, Elizabeth

    2017-01-01

    To the Editor: Extracting knowledge from the many types of big data produced by high-throughput methods remains a challenge, even when data are from Escherichia coli, the best characterized bacterial species. Here, we present iML1515, the most complete genome-scale reconstruction of the metabolic...... network in E. coli K-12 MG1655 to date, and we demonstrate how it can be used to address this challenge. Enabling analysis of several data types, including transcriptomes, proteomes, and metabolomes, iML1515 accounts for 1,515 open reading frames and 2,719 metabolic reactions involving 1,192 unique...

  11. Communicating Regional Geology and Geohazards to K-12 Teachers

    Science.gov (United States)

    Pratt-Sitaula, B.; Butler, R. F.; Whitman, J. M.; Granshaw, F. D.; Magura, B.; Hedeen, C.; Groom, R.; Thompson, D.; Johnson, J. A.

    2011-12-01

    The Teachers on the Leading Edge (TOTLE) program has designed an innovative model for middle school teacher professional development related to Pacific NW plate margin hazards and EarthScope science. The program has been effective at improving teacher knowledge and confidence and has led to high rates of curricular implementation. The elements particularly key to success are: a) facilitation team with broad expertise in both geoscience and education; b) regional team format that encouraged learning community development; c) teachers' desire to focus on regional geologic hazards; d) significant use of animations and field trips to aid in "visualization" of processes; and e) extensive "kit" of teaching materials for easy classroom transfer. The 1-week workshops were held in summer 2008-2010 and 35 Pacific NW middle school teachers attended each year. Geoscientists from universities and research institutions conducted the field trips and content sessions. Master K-12 Earth science teachers designed or modified curricular materials and led the teaching implementation sessions. Each year, the teachers were divided into 5 regional teams led by geoscience educator team leaders (community college instructors or similar). Teachers were surveyed on teaching confidence and content knowledge before and after the workshops. Follow-up surveys addressed teaching confidence and curricular implementation and were conducted 0.7 years after (all cohorts), 1.7 years after (2009 cohort), and 2.7 years after (2008 cohort). Teacher confidence (4-point scale: 1="not at all confident"; 4="very confident") on workshop content topics continued to rise in each subsequent survey from 2.7 (pre) to 3.3 (post) to 3.5 (0.7 yr follow up) to 3.7 (2-3 yr follow up) suggesting the program impact is long-lived. In the post-workshop surveys, 100% of participants agreed or strongly agreed that the program would positively impact their teaching. Average teacher performance on content questions improved

  12. Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Daniela Ledezma-Tejeida

    2017-08-01

    Full Text Available In the face of changes in their environment, bacteria adjust gene expression levels and produce appropriate responses. The individual layers of this process have been widely studied: the transcriptional regulatory network describes the regulatory interactions that produce changes in the metabolic network, both of which are coordinated by the signaling network, but the interplay between them has never been described in a systematic fashion. Here, we formalize the process of detection and processing of environmental information mediated by individual transcription factors (TFs, utilizing a concept termed genetic sensory response units (GENSOR units, which are composed of four components: (1 a signal, (2 signal transduction, (3 genetic switch, and (4 a response. We used experimentally validated data sets from two databases to assemble a GENSOR unit for each of the 189 local TFs of Escherichia coli K-12 contained in the RegulonDB database. Further analysis suggested that feedback is a common occurrence in signal processing, and there is a gradient of functional complexity in the response mediated by each TF, as opposed to a one regulator/one pathway rule. Finally, we provide examples of other GENSOR unit applications, such as hypothesis generation, detailed description of cellular decision making, and elucidation of indirect regulatory mechanisms.

  13. Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli

    Science.gov (United States)

    Ledezma-Tejeida, Daniela; Ishida, Cecilia; Collado-Vides, Julio

    2017-01-01

    In the face of changes in their environment, bacteria adjust gene expression levels and produce appropriate responses. The individual layers of this process have been widely studied: the transcriptional regulatory network describes the regulatory interactions that produce changes in the metabolic network, both of which are coordinated by the signaling network, but the interplay between them has never been described in a systematic fashion. Here, we formalize the process of detection and processing of environmental information mediated by individual transcription factors (TFs), utilizing a concept termed genetic sensory response units (GENSOR units), which are composed of four components: (1) a signal, (2) signal transduction, (3) genetic switch, and (4) a response. We used experimentally validated data sets from two databases to assemble a GENSOR unit for each of the 189 local TFs of Escherichia coli K-12 contained in the RegulonDB database. Further analysis suggested that feedback is a common occurrence in signal processing, and there is a gradient of functional complexity in the response mediated by each TF, as opposed to a one regulator/one pathway rule. Finally, we provide examples of other GENSOR unit applications, such as hypothesis generation, detailed description of cellular decision making, and elucidation of indirect regulatory mechanisms. PMID:28824593

  14. Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome.

    Science.gov (United States)

    Hücker, Sarah M; Ardern, Zachary; Goldberg, Tatyana; Schafferhans, Andrea; Bernhofer, Michael; Vestergaard, Gisle; Nelson, Chase W; Schloter, Michael; Rost, Burkhard; Scherer, Siegfried; Neuhaus, Klaus

    2017-01-01

    In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set.

  15. Research and Practice in K-12 Online Learning: A Review of Open Access Literature

    Directory of Open Access Journals (Sweden)

    Cathy S. Cavanaugh

    2009-02-01

    Full Text Available The literature related to online learning programs for K-12 students dates to the mid-1990s and builds upon a century of research and practice from K-12 distance education. While K-12 online learning programs have evolved and grown over the past decade, the amount of published research on virtual schooling practice and policy is limited. The current literature includes practitioner reports and experimental and quasi-experimental studies, both published and unpublished. This paper reviews open access literature in K-12 online learning and reports on a structured content analysis of the documents. Themes in the literature include steady growth and a focus on the benefits, challenges, and broad effectiveness of K-12 online learning. In addition, newly developed standards for K-12 online learning are emerging in descriptions of effective practices.

  16. Development of a fast and easy method for Escherichia coli genome editing with CRISPR/Cas9.

    Science.gov (United States)

    Zhao, Dongdong; Yuan, Shenli; Xiong, Bin; Sun, Hongnian; Ye, Lijun; Li, Jing; Zhang, Xueli; Bi, Changhao

    2016-12-01

    Microbial genome editing is a powerful tool to modify chromosome in way of deletion, insertion or replacement, which is one of the most important techniques in metabolic engineering research. The emergence of CRISPR/Cas9 technique inspires various genomic editing methods. In this research, the goal of development of a fast and easy method for Escherichia coli genome editing with high efficiency is pursued. For this purpose, we designed modular plasmid assembly strategy, compared effects of different length of homologous arms for recombination, and tested different sets of recombinases. The final technique we developed only requires one plasmid construction and one transformation of practice to edit a genomic locus with 3 days and minimal lab work. In addition, the single temperature sensitive plasmid is easy to eliminate for another round of editing. Especially, process of the modularized editing plasmid construction only takes 4 h. In this study, we developed a fast and easy genome editing procedure based on CRISPR/Cas9 system that only required the work of one plasmid construction and one transformation, which allowed modification of a chromosome locus within 3 days and could be performed continuously for multiple loci.

  17. Content Management on the Internet: A look at K-12 schools access to resources

    OpenAIRE

    Wenrich, John Richard

    1998-01-01

    The Internet presents a new phenomenon to educators and students in the K-12 environment. It's ease of use and ready access to material provides an overwhelming resource for use in the K-12 classroom. This study looked at content management of Internet resources in the K-12 school environment. Content management is defined as the methods of organizing access to the information available on the Internet allowing the teacher to effectively use resources in a classroom setting. Teachers have man...

  18. E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Margie A Kinnersley

    2009-11-01

    Full Text Available Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguished evolved clones from their common ancestor. Using transcriptional profiling on co-evolved clones cultured separately under glucose-limitation we identified 180 genes significantly altered in expression relative to the common ancestor grown under similar conditions. Ninety of these were similarly expressed in all clones, and many of the genes affected (e.g., mglBAC, mglD, and lamB are in operons coordinately regulated by CRP and/or rpoS. While the remaining significant expression differences were clone-specific, 93% were exhibited by the majority clone, many of which are controlled by global regulators, CRP and CpxR. When transcriptional profiling was performed on adaptive clones cultured together, many expression differences that distinguished the majority clone cultured in isolation were absent, suggesting that CpxR may be activated by overflow metabolites removed by cross-feeding strains in co-culture. Relative to their common ancestor, shared expression differences among adaptive clones were partly attributable to early-arising shared mutations in the trans-acting global regulator, rpoS, and the cis-acting regulator, mglO. Gene expression differences that distinguished clones may in part be explained by mutations in trans-acting regulators malT and glpK, and in cis-acting sequences of acs. In the founder, a cis-regulatory mutation in acs (acetyl CoA synthetase and a structural mutation in glpR (glycerol-3-phosphate repressor likely favored evolution of specialists that thrive on overflow metabolites. Later-arising mutations that led to specialization

  19. Characterization of Campylobacter jejuni and Campylobacter coli Broiler Isolates by Whole-Genome Sequencing

    DEFF Research Database (Denmark)

    Cantero, Guillermo; Correa-Fiz, Florencia; Ronco, Troels

    2017-01-01

    -nucleotide polymorphisms showed two main cluster grouping strains by species. Phenotypic resistances to quinolones (100%), tetracycline (81%), streptomycin (75%), erythromycin (56%), and gentamicin (13%) were found. All the isolates carried the C257T point mutation in the subunit A of the DNA gyrase gene (Thr86Ile......) conferring resistance to quinolones, while all the isolates showing resistance to tetracycline carried the tet(O) gene. The genes aph(3′)-III and aadE conferring resistance to aminoglycosides were identified in the two isolates (one C. jejuni and one C. coli) resistant to streptomycin and gentamicin....... The point mutation A2075G on the 23S rDNA conferring high resistance to macrolides was detected in three C. coli isolates. The CmeABC multidrug efflux pump was also detected, both in C. jejuni and C. coli isolates. All C. jejuni and C. coli isolates were positive for most of the 34 virulence...

  20. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

    DEFF Research Database (Denmark)

    Grad, Yonatan H; Lipsitch, Marc; Feldgarden, Michael

    2012-01-01

    The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the ...... that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak....

  1. Improving genome annotation of enterotoxigenic Escherichia coli TW10598 by a label-free quantitative MS/MS approach.

    Science.gov (United States)

    Pettersen, Veronika Kuchařová; Steinsland, Hans; Wiker, Harald G

    2015-11-01

    The most commonly used genome annotation processes are to a great extent based on computational methods. However, those can only predict genes that have been described earlier or that have sequence signatures indicative of a gene function. Here, we report a synonymous proteogenomic approach for experimentally improving microbial genome annotation based on label-free quantitative MS/MS. The approach is exemplified by analysis of cell extracts from in vitro cultured enterotoxigenic Escherichia coli (ETEC) strain TW10598, as part of an effort to create a new reference ETEC genome sequence. The proteomic analysis yielded identification of 2060 proteins, out of which 312 proteins were originally described as hypothetical. For 84% of the identified proteins we have provided description of their relative quantitative levels, among others, for 20 abundantly expressed ETEC virulence factors. Proteogenomic mapping supported the existence of four protein-coding genes that had not been annotated, and led to correction of translation start positions of another nine. The addition of the proteomic analysis into TW10598 genome re-annotation project improved quality of the annotation, and provided experimental evidence for a significant portion of ETEC expressed proteome. Data are available via ProteomeXchange with identifier PXD002473 (http://proteomecentral.proteomexchange.org/dataset/PXD002473). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.

    Science.gov (United States)

    Monk, Jonathan M; Charusanti, Pep; Aziz, Ramy K; Lerman, Joshua A; Premyodhin, Ned; Orth, Jeffrey D; Feist, Adam M; Palsson, Bernhard Ø

    2013-12-10

    Genome-scale models (GEMs) of metabolism were constructed for 55 fully sequenced Escherichia coli and Shigella strains. The GEMs enable a systems approach to characterizing the pan and core metabolic capabilities of the E. coli species. The majority of pan metabolic content was found to consist of alternate catabolic pathways for unique nutrient sources. The GEMs were then used to systematically analyze growth capabilities in more than 650 different growth-supporting environments. The results show that unique strain-specific metabolic capabilities correspond to pathotypes and environmental niches. Twelve of the GEMs were used to predict growth on six differentiating nutrients, and the predictions were found to agree with 80% of experimental outcomes. Additionally, GEMs were used to predict strain-specific auxotrophies. Twelve of the strains modeled were predicted to be auxotrophic for vitamins niacin (vitamin B3), thiamin (vitamin B1), or folate (vitamin B9). Six of the strains modeled have lost biosynthetic pathways for essential amino acids methionine, tryptophan, or leucine. Genome-scale analysis of multiple strains of a species can thus be used to define the metabolic essence of a microbial species and delineate growth differences that shed light on the adaptation process to a particular microenvironment.

  3. Applying the Quadratic Usage Framework to Research on K-12 STEM Digital Learning Resources

    Science.gov (United States)

    Luetkemeyer, Jennifer R.

    2016-01-01

    Numerous policymakers have called for K-12 educators to increase their effectiveness by transforming science, technology, engineering, and mathematics (STEM) learning and teaching with digital resources and tools. In this study we outline the significance of studying pressing issues related to use of digital resources in the K-12 environment and…

  4. New Learning Models: The Evolution of Online Learning into Innovative K-12 Blended Programs

    Science.gov (United States)

    Patrick, Susan

    2011-01-01

    The author traces the growth of K-12 online learning in the United States from its modest genesis in the mid-1990s with 50,000 students to the more than 4 million enrollments today, the fastest scaling ever of any innovation in K-12 education. The evolution from one-size-fits-all online courses to innovative, blended instructional models that are…

  5. Virtual Schools: The Changing Landscape of K-12 Education in the U.S.

    Science.gov (United States)

    Toppin, Ian N.; Toppin, Sheila M.

    2016-01-01

    Virtual schools are a growing phenomenon in k-12 education. School systems in almost every state in the United States offer some version of fully online or blended education. It is no longer far-fetched to conclude that if the current trend continues, virtual school enrollments will eclipse those of traditional brick-and-mortar k-12 institutions…

  6. STEM Integration in K-12 Education: Status, Prospects, and an Agenda for Research

    Science.gov (United States)

    Honey, Margaret; Pearson, Greg; Schweingruber, Heidi

    2014-01-01

    "STEM Integration in K-12 Education" examines current efforts to connect the STEM disciplines in K-12 education. This report identifies and characterizes existing approaches to integrated STEM education, both in formal and after- and out-of-school settings. The report reviews the evidence for the impact of integrated approaches on…

  7. K-12 Teacher Perceptions Regarding the Flipped Classroom Model for Teaching and Learning

    Science.gov (United States)

    Gough, Evan; DeJong, David; Grundmeyer, Trent; Baron, Mark

    2017-01-01

    A great deal of evidence can be cited from higher education literature on the effectiveness of the flipped classroom; however, very little research was discovered on the flipped classroom at the K-12 level. This study examined K-12 teachers' perceptions regarding the flipped classroom and differences in teachers' perceptions based on grade level…

  8. Changes in K-12 Education: Implications for the BC Post-Secondary System

    Science.gov (United States)

    McQuarrie, Fiona A. E.

    2016-01-01

    It is generally assumed by educators that the K-12 curriculum--the curriculum used in primary, elementary, and secondary education--will affect students' post-secondary educational experiences and their ability to enter the workforce. This report takes a multi-faceted approach to addressing the impact of changes in the K-12 curriculum on students'…

  9. Exploring Arizona K-12 Virtual Educator Experiences and Perspectives Developing Collaborative Learning Communities

    Science.gov (United States)

    Cross, Deborah Iyron

    2015-01-01

    Arizona Online Instruction (AOI) provided an instructional alternative to nearly fifty thousand K-12 students in Arizona during the 2012-2013 school year. Growth in online education underscores the importance of evolving the role of the K-12 virtual teacher as the human agent (Turvey, 2008) demonstrating social learning theory (Bandura, 1977) by…

  10. Physical Education Teacher Educator's Perceptions toward and Understanding of K-12 Online Physical Education

    Science.gov (United States)

    Daum, David N.; Woods, Amelia M.

    2015-01-01

    K-12 online physical education (OLPE) is as an educational opportunity in at least 30 states in the US (NASPE, 2006; 2010; 2012). The purpose of this study was to examine physical education teacher educators' perceptions toward and understanding of K-12 OLPE. Bandura's Social Cognitive Theory (1986) served as the theoretical framework for this…

  11. An Exploratory Study on K-12 Teachers' Use of Technology and Multimedia in the Classroom

    Science.gov (United States)

    Martin, Florence; Carr, Marsha L.

    2015-01-01

    21st century has seen new technology and multimedia made available for integration in K-12 classrooms. This exploratory study examines K-12 teachers' use of technology and multimedia in the classroom in two southern counties in the Southeastern United States. The purpose of the study was to answer the following five research questions: 1) What…

  12. State P-20 Councils and Collaboration between K-12 and Higher Education

    Science.gov (United States)

    Rippner, Jennifer A.

    2017-01-01

    For decades, numerous observers have agreed on the value of collaboration between K-12 and higher education--especially as these sectors work toward increasing college readiness and success. While most states maintain separate agencies for K-12 and higher education, many states have worked to foster collaboration through state P-20 councils.…

  13. Development and Evaluation of Food Safety Modules for K-12 Science Education

    Science.gov (United States)

    Chapin, Travis K.; Pfuntner, Rachel C.; Stasiewicz, Matthew J.; Wiedmann, Martin; Orta-Ramirez, Alicia

    2015-01-01

    Career and educational opportunities in food science and food safety are underrecognized by K-12 students and educators. Additionally, misperceptions regarding nature of science understanding persist in K-12 students despite being emphasized as an important component of science education for over 100 y. In an effort to increase awareness…

  14. From Teacher to Teacher Educator: Should You Move from a K-12 Classroom into Higher Education?

    Science.gov (United States)

    Clement, Mary C.

    2011-01-01

    College teaching can be as rewarding as a K-12 career and, whether in elementary school or college, students deserve good teachers. College professors who prepare teachers can have a tremendous impact on K-12 classrooms for decades into the future. However, career paths vary widely, and the path to teaching in higher education is as unique as the…

  15. Value Added Models and the Implementation of the National Standards of K-12 Physical Education

    Science.gov (United States)

    Seymour, Clancy M.; Garrison, Mark J.

    2017-01-01

    The implementation of value-added models of teacher evaluation continue to expand in public education, but the effects of using student test scores to evaluate K-12 physical educators necessitates further discussion. Using the five National Standards for K-12 Physical Education from the Society of Health and Physical Educators America (SHAPE),…

  16. Development of an Attitude Scale to Assess K-12 Teachers' Attitudes toward Nanotechnology

    Science.gov (United States)

    Lan, Yu-Ling

    2012-01-01

    To maximize the contributions of nanotechnology to this society, at least 60 countries have put efforts into this field. In Taiwan, a government-funded K-12 Nanotechnology Programme was established to train K-12 teachers with adequate nanotechnology literacy to foster the next generation of Taiwanese people with sufficient knowledge in…

  17. Development of the Advanced Energy Design Guide for K-12 Schools -- 50% Energy Savings

    Energy Technology Data Exchange (ETDEWEB)

    Bonnema, E.; Leach, M.; Pless, S.; Torcellini, P.

    2013-02-01

    This Technical Support Document (TSD) describes the process and methodology for the development of the Advanced Energy Design Guide for K-12 School Buildings: Achieving 50% Energy Savings Toward a Net Zero Energy Building (AEDG-K12) (ASHRAE et al. 2011a). The AEDG-K12 provides recommendations for achieving 50% whole-building energy savings in K-12 schools over levels achieved by following ANSI/ASHRAE/IESNA Standard 90.1-2004, Energy Standard for Buildings Except Low-Rise Residential Buildings (Standard 90.1-2004) (ASHRAE 2004b). The AEDG-K12 was developed in collaboration with the American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE), the American Institute of Architects (AIA), the Illuminating Engineering Society of North America (IES), the U.S. Green Building Council (USGBC), and the U.S. Department of Energy (DOE).

  18. Draft Genome Sequence of Campylobacter jejuni CAM970 and C. coli CAM962, Associated with a Large Outbreak of Foodborne Illness in Fukuoka, Japan, in 2016.

    Science.gov (United States)

    Asakura, Hiroshi; Takahashi, Naoto; Yamamoto, Shiori; Maruyama, Hiroyuki

    2017-06-15

    Here, we report the draft genome sequences of Campylobacter jejuni CAM970 and C. coli CAM962, which were associated with a large outbreak of foodborne illness originating from undercooked chicken sushi in Fukuoka, Japan, in May 2016. Their genome sizes were 1,690,901 and 1,704,736 bp, with 22 and 23 rRNAs, 9 and 9 tRNAs, and 411× and 419× coverage for C. jejuni CAM970 and C. coli CAM962, respectively. Copyright © 2017 Asakura et al.

  19. Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system

    Directory of Open Access Journals (Sweden)

    Sandeep Ghatak

    2017-03-01

    Full Text Available Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States. WGS, de novo assembly, and annotation of the genome revealed a chromosome of 1,718,974 bp and a mega-plasmid (pCOS502 of 125,964 bp. GC content of the genome was 31.2% with 1931 coding sequences and 53 non-coding RNAs. Multiple virulence factors including a plasmid-borne type VI secretion system and antimicrobial resistance genes (beta-lactams, fluoroquinolones, and aminoglycoside were found. The presence of T6SS in a mobile genetic element (plasmid suggests plausible horizontal transfer of these virulence genes to other organisms. The C. coli YH502 genome also harbors CRISPR sequences and associated proteins. Phylogenetic analysis based on average nucleotide identity and single nucleotide polymorphisms identified closely related C. coli genomes available in the NCBI database. Taken together, the analyzed genomic data of this potentially virulent strain of C. coli will facilitate further understanding of this important foodborne pathogen most likely leading to better control strategies. The chromosome and plasmid sequences of C. coli YH502 have been deposited in GenBank under the accession numbers CP018900.1 and CP018901.1, respectively.

  20. Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system.

    Science.gov (United States)

    Ghatak, Sandeep; He, Yiping; Reed, Sue; Strobaugh, Terence; Irwin, Peter

    2017-03-01

    Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States. WGS, de novo assembly, and annotation of the genome revealed a chromosome of 1,718,974 bp and a mega-plasmid (pCOS502) of 125,964 bp. GC content of the genome was 31.2% with 1931 coding sequences and 53 non-coding RNAs. Multiple virulence factors including a plasmid-borne type VI secretion system and antimicrobial resistance genes (beta-lactams, fluoroquinolones, and aminoglycoside) were found. The presence of T6SS in a mobile genetic element (plasmid) suggests plausible horizontal transfer of these virulence genes to other organisms. The C. coli YH502 genome also harbors CRISPR sequences and associated proteins. Phylogenetic analysis based on average nucleotide identity and single nucleotide polymorphisms identified closely related C. coli genomes available in the NCBI database. Taken together, the analyzed genomic data of this potentially virulent strain of C. coli will facilitate further understanding of this important foodborne pathogen most likely leading to better control strategies. The chromosome and plasmid sequences of C. coli YH502 have been deposited in GenBank under the accession numbers CP018900.1 and CP018901.1, respectively.

  1. E. coli

    Science.gov (United States)

    Liang, Xiao; Liao, Chunyu; Thompson, Michael L; Soupir, Michelle L; Jarboe, Laura R; Dixon, Philip M

    2016-01-01

    The importance of E. coli as an indicator organism in fresh water has led to numerous studies focusing on cell properties and transport behavior. However, previous studies have been unable to assess if differences in E. coli cell surface properties and genomic variation are associated with different environmental habitats. In this study, we investigated the variation in characteristics of E. coli obtained from stream water and stream bottom sediments. Cell properties were measured for 77 genomically different E. coli strains (44 strains isolated from sediments and 33 strains isolated from water) under common stream conditions in the Upper Midwestern United States: pH 8.0, ionic strength 10 mM and 22°C. Measured cell properties include hydrophobicity, zeta potential, net charge, total acidity, and extracellular polymeric substance (EPS) composition. Our results indicate that stream sediment E. coli had significantly greater hydrophobicity, greater EPS protein content and EPS sugar content, less negative net charge, and higher point of zero charge than stream water E. coli . A significant positive correlation was observed between hydrophobicity and EPS protein for stream sediment E. coli but not for stream water E. coli . Additionally, E. coli surviving in the same habitat tended to have significantly larger (GTG) 5 genome similarity. After accounting for the intrinsic impact from the genome, environmental habitat was determined to be a factor influencing some cell surface properties, such as hydrophobicity. The diversity of cell properties and its resulting impact on particle interactions should be considered for environmental fate and transport modeling of aquatic indicator organisms such as E. coli .

  2. Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli (APEC).

    Science.gov (United States)

    Lee, Jung Seok; Jang, Ho Bin; Kim, Ki Sei; Kim, Tae Hwan; Im, Se Pyeong; Kim, Si Won; Lazarte, Jassy Mary S; Kim, Jae Sung; Jung, Tae Sung

    2015-01-01

    Avian pathogenic Escherichia coli (APEC) is a major pathogen that causes avian colibacillosis and is associated with severe economic losses in the chicken-farming industry. Here, bacteriophage KBNP1315, infecting APEC strain KBP1315, was genomically and functionally characterized. The evolutionary relationships of KBNP1315 were analyzed at the genomic level using gene (protein)-sharing networks, the Markov clustering (MCL) algorithm, and comparative genomics. Our network analysis showed that KBNP1315 was connected to 30 members of the Autographivirinae subfamily, which comprises the SP6-, T7-, P60-, phiKMV-, GAP227- and KP34-related groups. Network decomposition suggested that KBNP1315 belongs to the SP6-like phages, but our comparison of putative encoded proteins revealed that key proteins of KBNP1315, including the tail spike protein and endolysin, had relative low levels of amino acid sequence similarity with other members of the SP6-like phages. Thus KBNP1315 may only be distantly related to the SP6-like phages, and (based on the difference in endolysin) its lysis mechanism may differ from theirs. To characterize the lytic functions of the holin and endolysin proteins from KBNP1315, we expressed these proteins individually or simultaneously in E. coli BL21 (DE3) competent cell. Interestingly, the expressed endolysin was secreted into the periplasm and caused a high degree of host cell lysis that was dose-dependently delayed/blocked by NaN3-mediated inhibition of the SecA pathway. The expressed holin triggered only a moderate inhibition of cell growth, whereas coexpression of holin and endolysin enhanced the lytic effect of endolysin. Together, these results revealed that KBNP1315 appears to use a pin-holin/signal-arrest-release (SAR) endolysin pathway to trigger host cell lysis.

  3. Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli (APEC.

    Directory of Open Access Journals (Sweden)

    Jung Seok Lee

    Full Text Available Avian pathogenic Escherichia coli (APEC is a major pathogen that causes avian colibacillosis and is associated with severe economic losses in the chicken-farming industry. Here, bacteriophage KBNP1315, infecting APEC strain KBP1315, was genomically and functionally characterized. The evolutionary relationships of KBNP1315 were analyzed at the genomic level using gene (protein-sharing networks, the Markov clustering (MCL algorithm, and comparative genomics. Our network analysis showed that KBNP1315 was connected to 30 members of the Autographivirinae subfamily, which comprises the SP6-, T7-, P60-, phiKMV-, GAP227- and KP34-related groups. Network decomposition suggested that KBNP1315 belongs to the SP6-like phages, but our comparison of putative encoded proteins revealed that key proteins of KBNP1315, including the tail spike protein and endolysin, had relative low levels of amino acid sequence similarity with other members of the SP6-like phages. Thus KBNP1315 may only be distantly related to the SP6-like phages, and (based on the difference in endolysin its lysis mechanism may differ from theirs. To characterize the lytic functions of the holin and endolysin proteins from KBNP1315, we expressed these proteins individually or simultaneously in E. coli BL21 (DE3 competent cell. Interestingly, the expressed endolysin was secreted into the periplasm and caused a high degree of host cell lysis that was dose-dependently delayed/blocked by NaN3-mediated inhibition of the SecA pathway. The expressed holin triggered only a moderate inhibition of cell growth, whereas coexpression of holin and endolysin enhanced the lytic effect of endolysin. Together, these results revealed that KBNP1315 appears to use a pin-holin/signal-arrest-release (SAR endolysin pathway to trigger host cell lysis.

  4. Using comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis.

    Science.gov (United States)

    Baumler, David J; Banta, Lois M; Hung, Kai F; Schwarz, Jodi A; Cabot, Eric L; Glasner, Jeremy D; Perna, Nicole T

    2012-01-01

    Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students' ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula.

  5. Draft Genome Sequences of Colistin-Resistant MCR-1-Producing Escherichia coli ST1850 and ST74 Strains Isolated from Commercial Chicken Meat.

    Science.gov (United States)

    Monte, Daniel F; Fernandes, Miriam R; Cerdeira, Louise; de Souza, Tiago A; Mem, Andressa; Franco, Bernadette D G M; Landgraf, Mariza; Lincopan, Nilton

    2017-05-18

    We present here the draft genome sequences of two colistin-resistant mcr-1-carrying Escherichia coli strains belonging to sequence type 74 (ST74) and ST1850, isolated from commercial chicken meat in Brazil. Assembly of this draft genome resulted in 5,022,083 and 4,950,681 bp, respectively, revealing the presence of the IncX4 plasmid-mediated mcr-1 gene responsible for resistance to colistin. Copyright © 2017 Monte et al.

  6. The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle.

    Science.gov (United States)

    Barth, Stefanie A; Menge, Christian; Eichhorn, Inga; Semmler, Torsten; Wieler, Lothar H; Pickard, Derek; Belka, Ariane; Berens, Christian; Geue, Lutz

    2016-09-01

    Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STEC(per)) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STEC(spo)) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STEC(per) isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STEC(spo) isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STEC(per) isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STEC(spo) isolates. Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STEC(per) from STEC(spo) isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level. Ruminants, especially cattle, are sources of food-borne infections by Shiga toxin-producing Escherichia coli (STEC) in humans. Some STEC strains persist in cattle for longer periods of time, while others are detected only sporadically. Persisting

  7. Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin

    Science.gov (United States)

    Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. O145 is recognized as one of the six non-O157 serotypes that are most frequently assoc...

  8. The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase

    Science.gov (United States)

    Shimada, Tomohiro; Tanaka, Kan

    2017-01-01

    The promoter selectivity of Escherichia coli RNA polymerase (RNAP) is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the sigma subunit, each recognizing a specific set of promoters. For identification of the “constitutive promoters” that are recognized by each RNAP holoenzyme alone in the absence of other supporting factors, we have performed the genomic SELEX screening in vitro for their binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of constitutive promoters for each RNAP holoenzyme was then estimated based on the location of RNAP-binding sites. The first successful screening of the constitutive promoters was achieved for RpoD (σ70), the principal sigma for transcription of growth-related genes. As an extension, we performed in this study the screening of constitutive promoters for four minor sigma subunits, stationary-phase specific RpoS (σ38), heat-shock specific RpoH (σ32), flagellar-chemotaxis specific RpoF (σ28) and extra-cytoplasmic stress-response RpoE (σ24). The total number of constitutive promoters were: 129~179 for RpoS; 101~142 for RpoH; 34~41 for RpoF; and 77~106 for RpoE. The list of constitutive promoters were compared with that of known promoters identified in vivo under various conditions and using varieties of E. coli strains, altogether allowing the estimation of “inducible promoters” in the presence of additional supporting factors. PMID:28666008

  9. The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase.

    Directory of Open Access Journals (Sweden)

    Tomohiro Shimada

    Full Text Available The promoter selectivity of Escherichia coli RNA polymerase (RNAP is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the sigma subunit, each recognizing a specific set of promoters. For identification of the "constitutive promoters" that are recognized by each RNAP holoenzyme alone in the absence of other supporting factors, we have performed the genomic SELEX screening in vitro for their binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of constitutive promoters for each RNAP holoenzyme was then estimated based on the location of RNAP-binding sites. The first successful screening of the constitutive promoters was achieved for RpoD (σ70, the principal sigma for transcription of growth-related genes. As an extension, we performed in this study the screening of constitutive promoters for four minor sigma subunits, stationary-phase specific RpoS (σ38, heat-shock specific RpoH (σ32, flagellar-chemotaxis specific RpoF (σ28 and extra-cytoplasmic stress-response RpoE (σ24. The total number of constitutive promoters were: 129~179 for RpoS; 101~142 for RpoH; 34~41 for RpoF; and 77~106 for RpoE. The list of constitutive promoters were compared with that of known promoters identified in vivo under various conditions and using varieties of E. coli strains, altogether allowing the estimation of "inducible promoters" in the presence of additional supporting factors.

  10. Genomic distribution of the small multidrug resistance protein EmrE over 29 Escherichia coli strains reveals two forms of the protein

    NARCIS (Netherlands)

    Kolbusz, Magdalena A.; Slotboom, Dirk J.; Lolkema, Juke S.

    Analysis of the genomes of 29 Escherichia coli strains revealed two different versions of the EmrE protein, a member of the small multidrug resistance family. The versions are different in length and contain 110 residues (EMRE110) and 165 residues (EMRE165). The N-terminal extension found in the

  11. Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut

    DEFF Research Database (Denmark)

    Porse, Andreas; Gumpert, Heidi; Kubicek-Sutherland, Jessica Z.

    2017-01-01

    Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of Escherichia coli in controlled laboratory environments, less effort has bee...

  12. Draft genome sequences of Escherichia coli O113:H21 strains recovered from a major produce-production region in California

    Science.gov (United States)

    Shiga toxin-producing Escherichia coli is a foodborne and waterborne pathogen and is responsible for outbreaks of human gastroenteritis. This report documents the draft genome sequences of seven O113:H21 strains recovered from livestock, wildlife, and soil samples collected in a major agricultural r...

  13. EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model.

    Science.gov (United States)

    Hädicke, Oliver; Klamt, Steffen

    2017-01-03

    Genome-scale metabolic modeling has become an invaluable tool to analyze properties and capabilities of metabolic networks and has been particularly successful for the model organism Escherichia coli. However, for several applications, smaller metabolic (core) models are needed. Using a recently introduced reduction algorithm and the latest E. coli genome-scale reconstruction iJO1366, we derived EColiCore2, a model of the central metabolism of E. coli. EColiCore2 is a subnetwork of iJO1366 and preserves predefined phenotypes including optimal growth on different substrates. The network comprises 486 metabolites and 499 reactions, is accessible for elementary-modes analysis and can, if required, be further compressed to a network with 82 reactions and 54 metabolites having an identical solution space as EColiCore2. A systematic comparison of EColiCore2 with its genome-scale parent model iJO1366 reveals that several key properties (flux ranges, reaction essentialities, production envelopes) of the central metabolism are preserved in EColiCore2 while it neglects redundancies along biosynthetic routes. We also compare calculated metabolic engineering strategies in both models and demonstrate, as a general result, how intervention strategies found in a core model allow the identification of valid strategies in a genome-scale model. Overall, EColiCore2 holds promise to become a reference model of E. coli's central metabolism.

  14. Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach

    Directory of Open Access Journals (Sweden)

    Mondal SI

    2015-12-01

    Full Text Available Shakhinur Islam Mondal,1,6,* Sabiha Ferdous,1,* Nurnabi Azad Jewel,1 Arzuba Akter,2,6 Zabed Mahmud,1 Md Muzahidul Islam,1 Tanzila Afrin,3 Nurul Karim4,5 1Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh; 2Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh; 3Department of Pharmacy, East West University, Aftabnagar, Bangladesh; 4Biochemistry and Molecular Biology Department, Jahangirnagar University, Savar, Bangladesh; 5Division of Parasitology, 6Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan *These authors contributed equally to this work Abstract: Bacterial enteric infections resulting in diarrhea, dysentery, or enteric fever constitute a huge public health problem, with more than a billion episodes of disease annually in developing and developed countries. In this study, the deadly agent of hemorrhagic diarrhea and hemolytic uremic syndrome, Escherichia coli O157:H7 was investigated with extensive computational approaches aimed at identifying novel and broad-spectrum antibiotic targets. A systematic in silico workflow consisting of comparative genomics, metabolic pathways analysis, and additional drug prioritizing parameters was used to identify novel drug targets that were essential for the pathogen’s survival but absent in its human host. Comparative genomic analysis of Kyoto Encyclopedia of Genes and Genomes annotated metabolic pathways identified 350 putative target proteins in E. coli O157:H7 which showed no similarity to human proteins. Further bioinformatic approaches including prediction of subcellular localization, calculation of molecular weight, and web-based investigation of 3D structural characteristics greatly aided in filtering the potential drug targets from 350 to 120. Ultimately, 44 non-homologous essential proteins of E

  15. Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal PathogenicEscherichia coli(ExPEC) Lineages.

    Science.gov (United States)

    Shaik, Sabiha; Ranjan, Amit; Tiwari, Sumeet K; Hussain, Arif; Nandanwar, Nishant; Kumar, Narender; Jadhav, Savita; Semmler, Torsten; Baddam, Ramani; Islam, Mohammed Aminul; Alam, Munirul; Wieler, Lothar H; Watanabe, Haruo; Ahmed, Niyaz

    2017-10-24

    Escherichia coli sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 ( n = 12), ST405 ( n = 10), and ST648 ( n = 18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage. IMPORTANCE E. coli , particularly the ST131 extraintestinal pathogenic E. coli (ExPEC) lineage, is an important cause of community- and

  16. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli

    DEFF Research Database (Denmark)

    Joensen, Katrine Grimstrup; Scheutz, Flemming; Lund, Ole

    2014-01-01

    was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing......Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming...... cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all...

  17. The Role of Extension Specialists in Meeting K-12 Science Education Goals.

    Science.gov (United States)

    Milam, Michael R.

    1996-01-01

    Describes a variety of ways in which extension specialists can support and supplement the K-12 science curriculum in Missouri. Includes a description of the Missouri Mastery Achievement Test (MMAT) and its use in assessing agricultural literacy. (DDR)

  18. Fostering Transformative Learning in an Online ESL Professional Development Program for K-12 Teachers

    National Research Council Canada - National Science Library

    Karin Sprow Forte; David Blouin

    2016-01-01

      This qualitative study examines evidence of transformative learning surrounding sociocultural issues in the K-12 classroom of in-service teachers, while participating in an online English as a Second Language (ESL...

  19. K12 Education Program Lessons Learned at the Center for Earthquake Research and Information

    Science.gov (United States)

    Patterson, G. L.; Dry, M.

    2003-12-01

    The Center for Earthquake Research and Information at the University of Memphis has been committed to increasing awareness for Seismic Hazard, Earthquake Engineering, and Earth Science among Mid-America's policy-makers, engineers, emergency managers, the general public, and K-12 teachers and students for nearly three decades. During that time we have learned many lessons related to providing effective education and outreach programs, especially for K-12 students. The lessons learned from these activities may be particularly appropriate for other regions where large earthquakes occur infrequently but have disproportionately high consequence areas due to low attenuation of seismic waves. Effective education programs in these settings must provide a consistent message across many states to a wide variety of socio-economic groups and professional communities through the leveraged resources of various groups and agencies. It is also beneficial to hire and train staff with K-12 teaching experience to work directly K-12 education organizations, and science curriculum coordinators.

  20. Engaging Scientists in NASA Education and Public Outreach: K - 12 Formal Education

    Science.gov (United States)

    Bartolone, Lindsay; Smith, D. A.; Eisenhamer, B.; Lawton, B. L.; Universe Professional Development Collaborative, Multiwavelength; NASA Data Collaborative, Use of; SEPOF K-12 Formal Education Working Group; E/PO Community, SMD

    2014-01-01

    The NASA Science Education and Public Outreach Forums support the NASA Science Mission Directorate (SMD) and its education and public outreach (E/PO) community through a coordinated effort to enhance the coherence and efficiency of SMD-funded E/PO programs. The Forums foster collaboration between scientists with content expertise and educators with pedagogy expertise. We present opportunities for the astronomy community to participate in collaborations supporting the NASA SMD efforts in the K - 12 Formal Education community. Members of the K - 12 Formal Education community include classroom educators, homeschool educators, students, and curriculum developers. The Forums’ efforts for the K - 12 Formal Education community include a literature review, appraisal of educators’ needs, coordination of audience-based NASA resources and opportunities, professional development, and support with the Next Generation Science Standards. Learn how to join in our collaborative efforts to support the K - 12 Formal Education community based upon mutual needs and interests.

  1. A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version

    Energy Technology Data Exchange (ETDEWEB)

    Price, M.; Raju, M.; Taylor, R.

    1993-01-01

    This report summarizes the reactions that occur in some of the principal metabolic pathways of E. coli. These pathways have been encoded as objects in GenoBase, an integrated database under development at Argonne National Laboratory in collaboration with researchers at the National Institutes of Health and at Harvard University. The report lists the substrates, products, enzymes, and cofactors for each pathway as a whole, followed by a detailed description of each reaction in the pathway. In addition, for each enzyme, the report displays a description and activity as listed in the Enzyme Data Bank, followed by the corresponding Swiss Protein Data Bank entries. Separate summary lines are included for each of the E. coli genes associated with each enzyme.

  2. Zero Energy Schools: Designing for the Future: Zero Energy Ready K-12 Schools

    Energy Technology Data Exchange (ETDEWEB)

    Torcellini, Paul A [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-09-29

    Designing, building, and operating zero energy ready K-12 schools provides benefits for districts, students, and teachers. Optimizing energy efficiency is important in any building, but it's particularly important in K-12 schools. Many U.S. school districts struggle for funding, and improving a school building's energy efficiency can free up operational funds that may then be available for educational and other purposes.

  3. Development of an Attitude Scale to Assess K-12 Teachers' Attitudes toward Nanotechnology

    Science.gov (United States)

    Lan, Yu-Ling

    2012-05-01

    To maximize the contributions of nanotechnology to this society, at least 60 countries have put efforts into this field. In Taiwan, a government-funded K-12 Nanotechnology Programme was established to train K-12 teachers with adequate nanotechnology literacy to foster the next generation of Taiwanese people with sufficient knowledge in nanotechnology. In the present study, the Nanotechnology Attitude Scale for K-12 teachers (NAS-T) was developed to assess K-12 teachers' attitudes toward nanotechnology. The NAS-T included 23 Likert-scale items that can be grouped into three components: importance of nanotechnology, affective tendencies in science teaching, and behavioural tendencies to teach nanotechnology. A sample of 233 K-12 teachers who have participated in the K-12 Nanotechnology Programme was included in the present study to investigate the psychometric properties of the NAS-T. The exploratory factor analysis of this teacher sample suggested that the NAS-T was a three-factor model that explained 64.11% of the total variances. This model was also confirmed by the confirmatory factor analysis to validate the factor structure of the NAS-T. The Cronbach's alpha values of three NAS-T subscales ranged from 0.89 to 0.95. Moderate to strong correlations among teachers' NAS-T domain scores, self-perception of own nanoscience knowledge, and their science-teaching efficacy demonstrated good convergent validity of the NAS-T. As a whole, psychometric properties of the NAS-T indicated that this instrument is an effective instrument for assessing K-12 teachers' attitudes toward nanotechnology. The NAS-T will serve as a valuable tool to evaluate teachers' attitude changes after participating in the K-12 Nanotechnology Programme.

  4. The ST131 Escherichia coli H22 subclone from human intestinal microbiota: Comparison of genomic and phenotypic traits with those of the globally successful H30 subclone.

    Science.gov (United States)

    Nicolas-Chanoine, Marie-Hélène; Petitjean, Marie; Mora, Azucena; Mayer, Noémie; Lavigne, Jean-Philippe; Boulet, Olivier; Leflon-Guibout, Véronique; Blanco, Jorge; Hocquet, Didier

    2017-03-27

    In 2006, we found healthy subjects carrying ST131 Escherichia coli in their intestinal microbiota consisting of two populations: a subdominant population of fluoroquinolone-resistant E. coli belonging to subclone H30 (H30-R or subclade C1), the current worldwide dominant ST131 subclone, and a dominant E. coli population composed of antibiotic-susceptible E. coli belonging to subclone H22 (clade B), the precursor of subclone H30. We sequenced the whole genome of fecal H22 strain S250, compared it to the genomes of ExPEC ST131 H30-Rx strain JJ1886 and commensal ST131 H41 strain SE15, sought the H22-H30 genomic differences in our fecal strains and assessed their phenotypic consequences. We detected 173 genes found in the Virulence Factor Database, of which 148 were shared by the three ST131 genomes, whereas some were genome-specific, notably those allowing determination of virotype (D for S250 and C for JJ1886). We found three sequences of the FimH site involved in adhesion: two in S250 and SE15 close and identical, respectively, to that previously reported to confer strong intestinal adhesion, and one in JJ1886, corresponding to that commonly present in uropathogenic E. coli. Among the genes involved in sugar metabolism, one encoding a gluconate kinase lacked in S250 and JJ1886. Although this gene was also absent in both our fecal H22 and H30-R strains, H22 strains showed a higher capacity to grow in minimal medium with gluconate. Among the genes involved in gluconate metabolism, only the ghrB gene differed between S250/H22 and JJ1886/H30-R strains, resulting in different gluconate reductases. Of the genes involved in biofilm formation, two were absent in the three genomes and one, fimB, in the JJ1886 genome. Our fecal H30-R strains lacking intact fimB displayed delayed biofilm formation relative to our fecal H22 strains. The H22 strains differed by subclade B type and plasmid content, whereas the H30-R strains were identical. Phenotypic analysis of our fecal strains

  5. Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes.

    Science.gov (United States)

    Chen, Yuansha; Mukherjee, Sampa; Hoffmann, Maria; Kotewicz, Michael L; Young, Shenia; Abbott, Jason; Luo, Yan; Davidson, Maureen K; Allard, Marc; McDermott, Patrick; Zhao, Shaohua

    2013-11-01

    Aminoglycoside resistance in Campylobacter has been routinely monitored in the United States in clinical isolates since 1996 and in retail meats since 2002. Gentamicin resistance first appeared in a single human isolate of Campylobacter coli in 2000 and in a single chicken meat isolate in 2007, after which it increased rapidly to account for 11.3% of human isolates and 12.5% of retail isolates in 2010. Pulsed-field gel electrophoresis analysis indicated that gentamicin-resistant C. coli isolates from retail meat were clonal. We sequenced the genomes of two strains of this clone using a next-generation sequencing technique in order to investigate the genetic basis for the resistance. The gaps of one strain were closed using optical mapping and Sanger sequencing, and this is the first completed genome of C. coli. The two genomes are highly similar to each other. A self-transmissible plasmid carrying multiple antibiotic resistance genes was revealed within both genomes, carrying genes encoding resistance to gentamicin, kanamycin, streptomycin, streptothricin, and tetracycline. Bioinformatics analysis and experimental results showed that gentamicin resistance was due to a phosphotransferase gene, aph(2")-Ig, not described previously. The phylogenetic relationship of this newly emerged clone to other Campylobacter spp. was determined by whole-genome single nucleotide polymorphisms (SNPs), which showed that it clustered with the other poultry isolates and was separated from isolates from livestock.

  6. In vitro biofilm formation of commensal and pathogenic Escherichia coli strains: impact of environmental and genetic factors

    DEFF Research Database (Denmark)

    Reisner, A.; Krogfelt, Karen; Klein, B.M.

    2006-01-01

    Our understanding of Escherichia coli biofilm formation in vitro is based on studies of laboratory K-12 strains grown in standard media. However, pathogenic E. coli isolates differ substantially in their genetic repertoire from E. coli K-12 and are subject to heterogeneous environmental condition...

  7. Simulation of the rate of transfer of antibiotic resistance between Escherichia coli strains cultured under well controlled environmental conditions

    NARCIS (Netherlands)

    Smelt, J.P.; Hoefsloot, H.C.; de Koster, C.G.; Schuurmans, J.M.; ter Kuile, B.H.; Brul, S.

    2015-01-01

    It was demonstrated that the tetracycline resistance plasmid in Escherichia coli resembling K-12 23:06 containing the E. coli plasmid DM0133 could be transferred to tetracycline sensitive E. coli K-12 MG1655 YFP. The sensitive recipient strain has a slight metabolic advantage in continuous

  8. The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli.

    Science.gov (United States)

    Esquerré, Thomas; Bouvier, Marie; Turlan, Catherine; Carpousis, Agamemnon J; Girbal, Laurence; Cocaign-Bousquet, Muriel

    2016-04-26

    Bacterial adaptation requires large-scale regulation of gene expression. We have performed a genome-wide analysis of the Csr system, which regulates many important cellular functions. The Csr system is involved in post-transcriptional regulation, but a role in transcriptional regulation has also been suggested. Two proteins, an RNA-binding protein CsrA and an atypical signaling protein CsrD, participate in the Csr system. Genome-wide transcript stabilities and levels were compared in wildtype E. coli (MG1655) and isogenic mutant strains deficient in CsrA or CsrD activity demonstrating for the first time that CsrA and CsrD are global negative and positive regulators of transcription, respectively. The role of CsrA in transcription regulation may be indirect due to the 4.6-fold increase in csrD mRNA concentration in the CsrA deficient strain. Transcriptional action of CsrA and CsrD on a few genes was validated by transcriptional fusions. In addition to an effect on transcription, CsrA stabilizes thousands of mRNAs. This is the first demonstration that CsrA is a global positive regulator of mRNA stability. For one hundred genes, we predict that direct control of mRNA stability by CsrA might contribute to metabolic adaptation by regulating expression of genes involved in carbon metabolism and transport independently of transcriptional regulation.

  9. Genomic and Transcriptomic Analysis of Escherichia coli Strains Associated with Persistent and Transient Bovine Mastitis and the Role of Colanic Acid.

    Science.gov (United States)

    Lippolis, John D; Holman, Devin B; Brunelle, Brian W; Thacker, Tyler C; Bearson, Bradley L; Reinhardt, Timothy A; Sacco, Randy E; Casey, Thomas A

    2018-01-01

    Escherichia coli is a leading cause of bacterial mastitis in dairy cattle. It is most often transient in nature, causing an infection that lasts 2 to 3 days. However, E. coli has been shown to cause a persistent infection in a minority of cases. Mechanisms that allow for a persistent E. coli infection are not fully understood. The goal of this work was to determine differences between E. coli strains originally isolated from dairy cattle with transient and persistent mastitis. Using RNA sequencing, we show gene expression differences in nearly 200 genes when bacteria from the two clinical phenotypes are compared. We sequenced the genomes of the E. coli strains and report genes unique to the two phenotypes. Differences in the wca operon, which encodes colanic acid, were identified by DNA as well as RNA sequencing and differentiated the two phenotypes. Previous work demonstrated that E. coli strains that cause persistent infections were more motile than those that cause transient infections. Deletion of genes in the wca operon from a persistent-infection strain resulted in a reduction of motility as measured in swimming and swarming assays. Furthermore, colanic acid has been shown to protect bacteria from complement-mediated killing. We show that transient-infection E. coli strains were more sensitive to complement-mediated killing. The deletion of genes from the wca operon caused a persistent-infection E. coli strain to become sensitive to complement-mediated killing. This work identifies important differences between E. coli strains that cause persistent and transient mammary infections in dairy cattle. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

  10. A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407

    Science.gov (United States)

    2010-11-01

    Vivienne Mahon,5 Carl Brinkley,6 Jon L. Hobman,7 Stephen J. Savarino,8 Susan M. Tumer ,4 Mark J. Pallen,9 Charles W. Penn,9 Julian Parkhill,1 A. Keith... Tumer ,1 Timothy J. Johnson,10 Nicholas R. Thomson,1 Stephen G. J. Smith,5 and Ian R. Henderson4* The We/lcome Trust Sanger Institute, Genome Campus

  11. Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids.

    Science.gov (United States)

    Losada, Liliana; DebRoy, Chitrita; Radune, Diana; Kim, Maria; Sanka, Ravi; Brinkac, Lauren; Kariyawasam, Subhashinie; Shelton, Daniel; Fratamico, Pina M; Kapur, Vivek; Feng, Peter C H

    2016-01-01

    The genomes of a diverse set of Escherichia coli, including many Shiga toxin-producing strains of various serotypes were determined. A total of 39 plasmids were identified among these strains, and many carried virulence or putative virulence genes of Shiga toxin-producing E. coli strains, virulence genes for other pathogenic E. coli groups, and some had combinations of these genes. Among the novel plasmids identified were eight that carried resistance genes to aminoglycosides, carbapenems, penicillins, cephalosporins, chloramphenicol, dihydrofolate reductase inhibitors, sulfonamides, tetracyclines and resistance to heavy metals. Two of the plasmids carried six of these resistance genes and two novel IncHI2 plasmids were also identified. The results of this study showed that plasmids carrying diverse resistance and virulence genes of various pathogenic E. coli groups can be found in E. coli strains and serotypes regardless of the isolate's source and therefore, is consistent with the premise that these mobile elements carrying these traits may be broadly disseminated among E. coli. Published by Elsevier Inc.

  12. Both genome and cytosol dynamics change in E. coli challenged with sublethal rifampicin

    Science.gov (United States)

    Wlodarski, Michal; Raciti, Bianca; Kotar, Jurij; Cosentino Lagomarsino, Marco; Fraser, Gillian M.; Cicuta, Pietro

    2017-02-01

    While the action of many antimicrobial drugs is well understood at the molecular level, a systems-level physiological response to antibiotics remains largely unexplored. This work considers fluctuation dynamics of both the chromosome and cytosol in Escherichia coli, and their response to sublethal treatments of a clinically important antibiotic, rifampicin. We precisely quantify the changes in dynamics of chromosomal loci and cytosolic aggregates (a rheovirus nonstructural protein known as μNS-GFP), measuring short time-scale displacements across several hours of drug exposure. To achieve this we develop an empirical method correcting for photo-bleaching and loci size effects. This procedure allows us to characterize the dynamic response to rifampicin in different growth conditions, including a customised microfluidic device. We find that sub-lethal doses of rifampicin cause a small but consistent increase in motility of both the chromosomal loci and cytosolic aggregates. Chromosomal and cytosolic responses are consistent with each other and between different growth conditions.

  13. Genome-wide analysis of E. coli cell-gene interactions

    DEFF Research Database (Denmark)

    Cardinale, S.; Cambray, G.

    2017-01-01

    modulate expression indirectly through an effect on cell size, putting forward the existence of a generic Size-Expression interaction in the model prokaryote Escherichia coli. Results: The Size-Expression interaction was quantified by inserting a dual fluorescent reporter gene construct into each......Background: The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even with the development of high-throughput screening methods and whole-cell models...... of the 3822 single-gene deletion strains comprised in the KEIO collection. Cellular size was measured for single cells via flow cytometry. Regression analyses were used to discriminate between expression-specific and gene-specific effects. Functions of the deleted genes broadly mapped onto three systems...

  14. Identification of novel isoprene synthases through genome mining and expression in Escherichia coli.

    Science.gov (United States)

    Ilmén, Marja; Oja, Merja; Huuskonen, Anne; Lee, Sangmin; Ruohonen, Laura; Jung, Simon

    2015-09-01

    Isoprene is a naturally produced hydrocarbon emitted into the atmosphere by green plants. It is also a constituent of synthetic rubber and a potential biofuel. Microbial production of isoprene can become a sustainable alternative to the prevailing chemical production of isoprene from petroleum. In this work, sequence homology searches were conducted to find novel isoprene synthases. Candidate sequences were functionally expressed in Escherichia coli and the desired enzymes were identified based on an isoprene production assay. The activity of three enzymes was shown for the first time: expression of the candidate genes from Ipomoea batatas, Mangifera indica, and Elaeocarpus photiniifolius resulted in isoprene formation. The Ipomoea batatas isoprene synthase produced the highest amounts of isoprene in all experiments, exceeding the isoprene levels obtained by the previously known Populus alba and Pueraria montana isoprene synthases that were studied in parallel as controls. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  15. The K-12 Educational Technology Value Chain: Apps for Kids, Tools for Teachers and Levers for Reform

    Science.gov (United States)

    Pierce, Glenn L.; Cleary, Paul F.

    2016-01-01

    Historically implementing, maintaining and managing educational technology has been difficult for K-12 educational systems. Consequently, opportunities for significant advances in K-12 education have often gone unrealized. With the maturation of Internet delivered services along with K-12 institutional trends, educational technologies are poised…

  16. Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant.

    Science.gov (United States)

    Crépin, Sébastien; Lamarche, Martin G; Garneau, Philippe; Séguin, Julie; Proulx, Julie; Dozois, Charles M; Harel, Josée

    2008-11-28

    Avian pathogenic E. coli (APEC) are associated with extraintestinal diseases in poultry. The pstSCAB-phoU operon belongs to the Pho regulon and encodes the phosphate specific transport (Pst) system. A functional Pst system is required for full virulence in APEC and other bacteria and contributes to resistance of APEC to serum, to cationic antimicrobial peptides and acid shock. The global mechanisms contributing to the attenuation and decreased resistance of the APEC pst mutant to environmental stresses have not been investigated at the transcriptional level. To determine the global effect of a pst mutation on gene expression, we compared the transcriptomes of APEC strain chi7122 and its isogenic pst mutant (K3) grown in phosphate-rich medium. Overall, 470 genes were differentially expressed by at least 1.5-fold. Interestingly, the pst mutant not only induced systems involved in phosphate acquisition and metabolism, despite phosphate availability, but also modulated stress response mechanisms. Indeed, transcriptional changes in genes associated with the general stress responses, including the oxidative stress response were among the major differences observed. Accordingly, the K3 strain was less resistant to reactive oxygen species (ROS) than the wild-type strain. In addition, the pst mutant demonstrated reduced expression of genes involved in lipopolysaccharide modifications and coding for cell surface components such as type 1 and F9 fimbriae. Phenotypic tests also established that the pst mutant was impaired in its capacity to produce type 1 fimbriae, as demonstrated by western blotting and agglutination of yeast cells, when compared to wild-type APEC strain chi7122. Overall, our data elucidated the effects of a pst mutation on the transcriptional response, and further support the role of the Pho regulon as part of a complex network contributing to phosphate homeostasis, adaptive stress responses, and E. coli virulence.

  17. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics

    Science.gov (United States)

    Downing, Tim

    2015-01-01

    High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)—a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols. PMID:27682088

  18. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics

    Directory of Open Access Journals (Sweden)

    Tim Downing

    2015-05-01

    Full Text Available High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131—a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.

  19. K-12 Teacher Understanding of Energy Conservation: Conceptual Metaphor, Dissipation, and Degradation

    Science.gov (United States)

    Daane, Abigail R.

    In K-12 educational settings, conservation of energy is typically presented in two ways: the conservation of energy principle (energy is neither created nor destroyed) and the sociopolitical need to conserve energy (we guard against energy being used up). These two meanings of conservation typically remain disconnected from each other and can appear contradictory, even after instruction. In an effort to support teachers in building robust understandings of energy from their existing knowledge, I designed a study to investigate the productive ideas in K-12 teachers' conversations about energy. A micro-analysis of discourse, gestures, and artifacts of professional development courses revealed teachers' productive ideas about three aspects of energy: conceptual metaphor, dissipation and degradation. In learning about energy, K-12 teachers come to use conceptual metaphors in their own language and value attending to students' metaphorical language as a means of formative assessment. Teachers' conversations about dissipation suggest that apparent difficulties with energy conservation may have their roots in a strong association between forms of energy (thermal) and their perceptible indicators (warmth). Teachers address this challenge by employing an exaggeration strategy to locate the dissipated thermal energy, making the energy indicator perceptible. Finally, teachers' unprompted statements about sociopolitical aspects of energy are related to both statements from the NGSS and aspects of energy degradation. I conclude that energy conservation can be better taught and learned in K-12 Education by: 1) understanding and applying conceptual metaphors about energy in K-12 settings, 2) using prior experiences to better understand dissipative energy processes involving imperceptible thermal energy, thereby understanding how energy conservation applies in all situations, and 3) connecting productive ideas about sociopolitical aspects of energy to canonical physics. Keywords

  20. Advanced Energy Retrofit Guide: Practical Ways to Improve Energy Performance, K-12 Schools (Book)

    Energy Technology Data Exchange (ETDEWEB)

    2013-02-01

    The U.S. Department of Energy developed the K-12 Advanced Energy Retrofit Guide to provide specific methodologies, information, and guidance to help energy managers and other stakeholders plan and execute energy efficiency improvements. We emphasize actionable information, practical methodologies, diverse case studies, and unbiased evaluation of the most promising retrofit measure for each building type. K-12 schools were selected as one of the highest priority building sectors, because schools affect the lives of most Americans. They also represent approximately 8% of the energy use and 10% of the floor area in commercial buildings.

  1. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

    DEFF Research Database (Denmark)

    Liu, Joanne K.; O’Brien, Edward J.; Lerman, Joshua A.

    2014-01-01

    cell morphology. Comparison of computations performed with this expanded ME-model, named iJL1678-ME, against available experimental data reveals that the model accurately describes translocation pathway expression and the functional proteome by compartmentalized mass. Conclusion: iJL1678-ME enables...... the functional content of membranes, cellular compartment-specific composition, and that it can be utilized to examine the effect of perturbing an expanded set of network components. iJL1678-ME takes a notable step towards the inclusion of cellular ultra-structure in genome-scale models....

  2. Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen

    Science.gov (United States)

    Grad, Yonatan H.; Godfrey, Paul; Cerquiera, Gustavo C.; Mariani-Kurkdjian, Patricia; Gouali, Malika; Bingen, Edouard; Shea, Terrence P.; Haas, Brian J.; Griggs, Allison; Young, Sarah; Zeng, Qiandong; Lipsitch, Marc; Waldor, Matthew K.; Weill, François-Xavier; Wortman, Jennifer R.; Hanage, William P.

    2013-01-01

    ABSTRACT The large outbreak of diarrhea and hemolytic uremic syndrome (HUS) caused by Shiga toxin-producing Escherichia coli O104:H4 in Europe from May to July 2011 highlighted the potential of a rarely identified E. coli serogroup to cause severe disease. Prior to the outbreak, there were very few reports of disease caused by this pathogen and thus little known of its diversity and evolution. The identification of cases of HUS caused by E. coli O104:H4 in France and Turkey after the outbreak and with no clear epidemiological links raises questions about whether these sporadic cases are derived from the outbreak. Here, we report genome sequences of five independent isolates from these cases and results of a comparative analysis with historical and 2011 outbreak isolates. These analyses revealed that the five isolates are not derived from the outbreak strain; however, they are more closely related to the outbreak strain and each other than to isolates identified prior to the 2011 outbreak. Over the short time scale represented by these closely related organisms, the majority of genome variation is found within their mobile genetic elements: none of the nine O104:H4 isolates compared here contain the same set of plasmids, and their prophages and genomic islands also differ. Moreover, the presence of closely related HUS-associated E. coli O104:H4 isolates supports the contention that fully virulent O104:H4 isolates are widespread and emphasizes the possibility of future food-borne E. coli O104:H4 outbreaks. PMID:23341549

  3. Comparative genomics and experimental evolution of Escherichia coli BL21(DE3) strains reveal the landscape of toxicity escape from membrane protein overproduction.

    Science.gov (United States)

    Kwon, Soon-Kyeong; Kim, Seong Keun; Lee, Dae-Hee; Kim, Jihyun F

    2015-11-04

    Achieving sufficient yields of proteins in their functional form represents the first bottleneck in contemporary bioscience and biotechnology. To accomplish successful overexpression of membrane proteins in a workhorse organism such as E. coli, defined and rational optimization strategies based on an understanding of the genetic background of the toxicity-escape mechanism are desirable. To this end, we sequenced the genomes of E. coli C41(DE3) and its derivative C43(DE3), which were developed for membrane protein production. Comparative analysis of their genomes with those of their ancestral strain E. coli BL21(DE3) revealed various genetic changes in both strains. A series of E. coli variants that are able to tolerate transformation with or overexpression of membrane proteins were generated by in vitro evolution. Targeted sequencing of the evolved strains revealed the mutational hotspots among the acquired genetic changes. By these combinatorial approaches, we found non-synonymous changes in the lac repressor gene of the lac operon as well as nucleotide substitutions in the lacUV5 promoter of the DE3 region, by which the toxic effect to the host caused by overexpression of membrane proteins could be relieved. A mutation in lacI was demonstrated to be crucial for conferring tolerance to membrane protein overexpression.

  4. Draft genome sequence of an O25:H4-ST131 Escherichia coli harbouring blaNDM-1 on an IncHI3 plasmid: A first report.

    Science.gov (United States)

    Subramanian, Gopalakrishnan Kaushik; Palani, Gnanasoundari; Vijayakumar, Ramanathan; Krishnan, Padma

    2017-03-01

    Carbapenem resistance conferred by New Delhi metallo-β-lactamases is mediated by plasmids of diverse incompatibility types harboured by different lineages of Enterobacteriaceae. In this study, we report the draft genome sequence of a ST131 Escherichia coli harbouring the blaNDM gene on an IncHI3 plasmid. Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

  5. Cellular chain formation in Escherichia coli biofilms

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk; Klemm, Per

    2009-01-01

    In this study we report on a novel structural phenotype in Escherichia coli biofilms: cellular chain formation. Biofilm chaining in E. coli K-12 was found to occur primarily by clonal expansion, but was not due to filamentous growth. Rather, chain formation was the result of intercellular......; type I fimbriae expression significantly reduced cellular chain formation, presumably by steric hindrance. Cellular chain formation did not appear to be specific to E coli K-12. Although many urinary tract infection (UTI) isolates were found to form rather homogeneous, flat biofilms, three isolates...

  6. Bacteriophage P1 pac sites inserted into the chromosome greatly increase packaging and transduction of Escherichia coli genomic DNA.

    Science.gov (United States)

    Huang, Haomin; Masters, Millicent

    2014-11-01

    The Escherichia coli bacteriophage P1 packages host chromosome separately from phage DNA, and transfers it to recipient cells at low frequency in a process called generalized transduction. Phage genomes are packaged from concatemers beginning at a specific site, pac. To increase transduction rate, we have inserted pac into the chromosome at up to five equally spaced positions; at least this many are fully tolerated in the absence of P1 infection. A single chromosomal pac greatly increases transduction of downstream markers without decreasing phage yields; 3.5 × as much total chromosomal DNA is packaged. Additional insertions decrease phage yield by > 90% and also decrease phage DNA synthesis, although less dramatically. Packaging of chromosomal markers near to and downstream of each inserted pac site is, at the same time, increased by greater than 10 fold. Transduction of markers near an inserted pac site can be increased by over 1000-fold, potentially allowing identification of such transductants by screening. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. K-12 Online Lesson Alignment to the Principles of Universal Design for Learning: The Khan Academy

    Science.gov (United States)

    Smith, Sean J.; Harvey, Evelyn E.

    2014-01-01

    The field of K-12 education is being transformed, with an influx of students, including those with identified disabilities, engaging in blended and fully online learning. While online learning shows promise for students with disabilities through flexible content and personalised instruction, concerns regarding accessibility and appropriateness of…

  8. A Nonverbal Language for Imagining and Learning: Dance Education in K-12 Curriculum

    Science.gov (United States)

    Hanna, Judith Lynne

    2008-01-01

    Curriculum theorists have provided a knowledge base concerning aesthetics, agency, creativity, lived experience, transcendence, learning through the body, and the power of the arts to engender visions of alternative possibilities in culture, politics, and the environment. However, these theoretical threads do not reveal the potential of K-12 dance…

  9. Exploring a Paperless Business Administrative System (BAS) Implementation in a K-12 School

    Science.gov (United States)

    Issa, Marwan M.

    2011-01-01

    The primary purpose of this qualitative study was to investigate how a paperless BAS can affect the overall performance of a school's administrative activities. The research included direct observation, survey questionnaires, document review, and both structured and unstructured interviews. The selected school, a K-12 charter school, was an ideal…

  10. Effects of a Haptic Augmented Simulation on K-12 Students' Achievement and Their Attitudes Towards Physics

    Science.gov (United States)

    Civelek, Turhan; Ucar, Erdem; Ustunel, Hakan; Aydin, Mehmet Kemal

    2014-01-01

    The current research aims to explore the effects of a haptic augmented simulation on students' achievement and their attitudes towards Physics in an immersive virtual reality environment (VRE). A quasi-experimental post-test design was employed utilizing experiment and control groups. The participants were 215 students from a K-12 school in…

  11. Job Satisfaction, Organizational Commitment, and Turnover Intention of Online Teachers in the K-12 Setting

    Science.gov (United States)

    Larkin, Ingle M.; Brantley-Dias, Laurie; Lokey-Vega, Anissa

    2016-01-01

    The purpose of this study was to measure and explore factors influencing K-12 online teachers' job satisfaction, organizational commitment, and turnover intentions. Using Maslow's Hierarchy of Needs (1954), Herzberg's Two-Factor Theory of Satisfaction (1959, 1968), Meyer and Allen's measure of Organizational Commitment (1997), and Fishbein and…

  12. Evaluating ICT Integration in Turkish K-12 Schools through Teachers' Views

    Science.gov (United States)

    Aydin, Mehmet Kemal; Gürol, Mehmet; Vanderlinde, Ruben

    2016-01-01

    The current study aims to explore ICT integration in Turkish K-12 schools purposively selected as a representation of F@tih and non-F@tih public schools together with a private school. A convergent mixed methods design was employed with a multiple case strategy as such it will enable to make casewise comparisons. The quantitative data was…

  13. School Hopscotch: A Comprehensive Review of K-12 Student Mobility in the United States

    Science.gov (United States)

    Welsh, Richard O.

    2017-01-01

    This article provides an integrative review of the extant literature on K-12 student mobility in the United States. Student mobility is a widespread phenomenon with significant policy implications. Changing schools is most prevalent among minority and low-income students in urban school districts. There is an ongoing debate about whether student…

  14. Limitations upon Legitimate Authority to Suspend and Expel K-12 Public School Students: A Moral Analysis

    Science.gov (United States)

    Ladenson, Robert F.

    2011-01-01

    This article presents a moral analysis of the limitations upon legitimate authority to suspend and expel students in K-12 public schools, and it brings this analysis to bear on a pair of difficult disciplinary cases. The analysis is grounded in a defense of a child's right to receive a public education. It identifies the minimum content of that…

  15. Monitoring Progress toward Successful K-12 STEM Education: A Nation Advancing?

    Science.gov (United States)

    National Academies Press, 2013

    2013-01-01

    Following a 2011 report by the National Research Council (NRC) on successful K-12 education in science, technology, engineering, and mathematics (STEM), Congress asked the National Science Foundation to identify methods for tracking progress toward the report's recommendations. In response, the NRC convened the Committee on an Evaluation Framework…

  16. Native Chinese-Speaking K-12 Language Teachers' Beliefs and Practices

    Science.gov (United States)

    Lü, Chan; Lavadenz, Magaly

    2014-01-01

    This study investigated the relationships between the beliefs and practices of K-12 native Chinese teachers on Chinese language and literacy instruction. Using a descriptive-exploratory design, this study employed a mixed-methods approach consisting of three steps: (1) a teacher beliefs questionnaire, (2) classroom observations and videotaping,…

  17. An Empirical Evaluation of Distance Learning's Effectiveness in the K-12 Setting

    Science.gov (United States)

    Harris-Packer, Jerilyn D.; Ségol, Geneviève

    2015-01-01

    This study evaluated the effect of online instruction on the academic achievement of K--12 students in ten states as measured by the percentage of proficient students in reading and mathematics at the school level. We used publicly available data provided by the Department of Education in Florida, Michigan, Minnesota, Nevada, Ohio, Pennsylvania,…

  18. Blueprint for Incorporating Service Learning: A Basic, Developmental, K-12 Service Learning Typology

    Science.gov (United States)

    Terry, Alice W.; Bohnenberger, Jann E.

    2004-01-01

    Citing the need for a basic, K-12 developmental framework for service learning, this article describes such a model. This model, an inclusive typology of service learning, distinguishes three levels of service learning: Community Service, Community Exploration, and Community Action. The authors correlate this typology to Piaget's cognitive…

  19. The Influence of Lean on K-12 District Management: A Case Study

    Science.gov (United States)

    Brown, Beverly

    2011-01-01

    For decades, policymakers and educators have focused on public school equity and adequacy, while paying little attention to efficiency. This qualitative single case study was designed to capture explicit information about Lean management, operations, and culture in a K-12 Michigan school district engaged in Lean training and implementation for a…

  20. Perceptions of Professional and Educational Skills Learning Opportunities Made Available through K-12 Robotics Programming

    Science.gov (United States)

    Bakke, Christine K.

    2013-01-01

    The purpose of this study is to examine whether participation in robotics provides opportunities for educational and professional skill development, significant enough to merit the recommendation of robotics courses as a part of mainstream curriculum offerings in K-12 schools. This non-experimental, mixed methods study examined current junior high…

  1. Dual Enrollment from Two Points of View: Higher Education and K-12

    Science.gov (United States)

    Kilgore, Wendy; Wagner, Ellen

    2017-01-01

    While dual enrollment fills a similar student success niche in both higher and K-12 education, the administrative perspectives of these two entities do not always align. This article highlights the groups' similarities and differences in perspective and proposes implications for practice.

  2. Plickers: A Formative Assessment Tool for K-12 and PETE Professionals

    Science.gov (United States)

    Krause, Jennifer M.; O'Neil, Kason; Dauenhauer, Brian

    2017-01-01

    Classroom response systems have become popular in K-12 and higher education settings in recent years in order to gauge student learning. The physical education environment is unique in that it is difficult to manage the technology associated with these systems, and therefore, student assessment can be cumbersome. A free classroom response system…

  3. The Chem-E-Car as a Vehicle for Service Learning through K-12 Outreach

    Science.gov (United States)

    Chirdon, William

    2017-01-01

    This article presents the results of combining the American Institute of Chemical Engineers' (AIChE) Chem-E-Car competition activities with engineering outreach to K-12 students in a service-learning course. Survey results are presented to show how the program develops technical skills as well as leadership, teamwork, and communication skills in…

  4. Online K-12 Teachers' Perceptions and Practices of Supporting Self-Regulated Learning

    Science.gov (United States)

    Huh, Yeol; Reigeluth, Charles M.

    2018-01-01

    With growing interest in and popularity of online learning and lifelong learners, students' ability to be engaged in self-regulated learning (SRL) has become more important. Moreover, online learning is becoming an important feature of K-12 education. Although SRL is known to be important and teachable, little research has been conducted on…

  5. Developing the Principal Technology Leadership Competency Indicators for Technical High Schools in K-12 in Taiwan

    Science.gov (United States)

    Shyr, Wen-Jye

    2017-01-01

    The purpose of this study was to develop principal technology leadership competency indicators for technical high schools in K-12 in Taiwan in order to improve the effectiveness of school administration and teaching. In the first part of the study, five experts in the technology leadership field are interviewed to explore the technology leadership…

  6. The Effect of Professional Development on Teacher Attitudes toward Online Learning in K-12 Education

    Science.gov (United States)

    Savakinas, Christy A.

    2012-01-01

    The purpose of this study was to examine how teacher attitudes toward online learning in K-12 education vary before, during, and after participation in a professional development program focused on ePedagogy and online course development. The study also examined which Key Design Factors, as identified by Wells (2007), influence teachers'…

  7. African Dance Aesthetics in a K-12 Dance Setting: From History to Social Justice

    Science.gov (United States)

    Ward, Sheila A.

    2013-01-01

    This article invites the reader to gain a deeper understanding of the aesthetics of African-based dance through the elements of tradition, transformation, and social justice. A discussion of the aesthetics of African dances within Africa and throughout the African diaspora opens the doors to present these dances in a K-12 setting, to explore a…

  8. Mixed Methods Evaluation of Statewide Implementation of Mathematics Education Technology for K-12 Students

    Science.gov (United States)

    Brasiel, Sarah; Martin, Taylor; Jeong, Soojeong; Yuan, Min

    2016-01-01

    An extensive body of research has demonstrated that the use in a K-12 classroom of technology, such as the Internet, computers, and software programs, enhances the learning of mathematics (Cheung & Slavin, 2013; Cohen & Hollebrands, 2011). In particular, growing empirical evidence supports that certain types of technology, such as…

  9. Technology-Related Strategies Used by Educational Leaders to Increase Prosocial Behavior in K-12 Schools

    Science.gov (United States)

    Beers, Jason Ronald

    2017-01-01

    Purpose. The purpose of this study was to identify technology-related strategies used by educational leaders to increase prosocial behavior in K-12 schools. Information and communication technology (ICT) is developing at a rapid rate and is becoming more ubiquitous among students. Discovering and understanding common technology-related strategies…

  10. Students Doing Chemistry: A Hand-On Experience for K-12

    Science.gov (United States)

    Selco, Jodye I.; Bruno, Mary; Chan, Sue

    2012-01-01

    A hands-on, minds-on inquiry chemistry experiment was developed for use in K-12 schools that enables students to combine the chemicals of their choice and observe the results. The chemistry involved is water based and builds upon acid-base, double displacement, and iodometric detection of starch reactions. Chemicals readily available in the…

  11. Netflixing Human Capital Development: Personalized Learning Technology and the Corporatization of K-12 Education

    Science.gov (United States)

    Roberts-Mahoney, Heather; Means, Alexander J.; Garrison, Mark J.

    2016-01-01

    Advanced by powerful venture philanthropies, educational technology companies, and the US Department of Education, a growing movement to apply "big data" through "learning analytics" to create "personalized learning" is currently underway in K-12 education in the United States. While scholars have offered various…

  12. Preparing University Students to Lead K-12 Engineering Outreach Programmes: A Design Experiment

    Science.gov (United States)

    Anthony, Anika B.; Greene, Howard; Post, Paul E.; Parkhurst, Andrew; Zhan, Xi

    2016-01-01

    This paper describes an engineering outreach programme designed to increase the interest of under-represented youth in engineering and to disseminate pre-engineering design challenge materials to K-12 educators and volunteers. Given university students' critical role as facilitators of the outreach programme, researchers conducted a two-year…

  13. A Study of the Tablet Computer's Application in K-12 Schools in China

    Science.gov (United States)

    Long, Taotao; Liang, Wenxin; Yu, Shengquan

    2013-01-01

    As an emerging mobile terminal, the tablet computer has begun to enter into the educational system. With the aim of having a better understanding of the application and people's perspectives on the new technology in K-12 schools in China, a survey was conducted to investigate the tablet computer's application, user's perspectives and requirements…

  14. Measurement Invariance of the "Servant Leadership Questionnaire" across K-12 Principal Gender

    Science.gov (United States)

    Xu, Lihua; Stewart, Trae; Haber-Curran, Paige

    2015-01-01

    Measurement invariance of the five-factor "Servant Leadership Questionnaire" between female and male K-12 principals was tested using multi-group confirmatory factor analysis. A sample of 956 principals (56.9% were females and 43.1% were males) was analysed in this study. The hierarchical multi-step measurement invariance test supported…

  15. K-12 Single-Sex Education: What Does the Research Say? ERIC Digest.

    Science.gov (United States)

    Haag, Pamela

    Although research on the effects of K-12 single-sex education is inconclusive in general, some common themes emerge in the research literature. This Digest reviews that research with particular attention to effects on girls' attitudes and achievement. The Digest first discusses attitudinal variables (i.e., self-esteem and attitudes toward academic…

  16. Leading Effective Educational Technology in K-12 School Districts: A Grounded Theory

    Science.gov (United States)

    Hill, Lara Gillian C.

    2011-01-01

    A systematic grounded theory qualitative study was conducted investigating the process of effectively leading educational technology in New Jersey public K-12 school districts. Data were collected from educational technology district leaders (whether formal or non-formal administrators) and central administrators through a semi-structured online…

  17. Using the van Hiele K-12 Geometry Learning Theory to Modify Engineering Mechanics Instruction

    Science.gov (United States)

    Sharp, Janet M.; Zachary, Loren W.

    2004-01-01

    Engineering students use spatial thinking when examining diagrams or models to study structure design. It is expected that most engineering students have solidified spatial thinking skills during K-12 schooling. However, according to what we know about geometry learning and teaching, spatial thinking probably needs to be explicitly taught within…

  18. Is K-12 Blended Learning Disruptive? An Introduction to the Theory of Hybrids

    Science.gov (United States)

    Christensen, Clayton M.; Horn, Michael B.; Staker, Heather

    2013-01-01

    The Clayton Christensen Institute for Disruptive Innovation, formerly the Innosight Institute, has published three papers describing the rise of K-12 blended learning--that is, formal education programs that combine online learning and brick-and-mortar schools. This fourth paper is the first to analyze blended learning through the lens of…

  19. Factors that Affect the Adoption and Use of Electronic Mail by K-12 Foreign Language Educators.

    Science.gov (United States)

    Shelley, Janine Onffroy

    1998-01-01

    Reports the results of electronic mail instruction given to K-12 foreign-language teachers during workshops. Factors found to influence workshop participants' adoption of email included training, the need to keep up with educational technology trends, availability of an easy-to-use system, hands-on experience, school support, and individual…

  20. A Longitudinal Evaluation Study of a Science Professional Development Program for K-12 Teachers: NERDS

    Science.gov (United States)

    Ewing-Taylor, Jacque M.

    2012-01-01

    A longitudinal evaluation study of a science professional development program for K-12 teachers was conducted using the CIPP evaluation model. Eleven years of program data were described and analyzed. Elementary teachers comprised 62% of the 384 participants, 17% of all participants were middle school teachers, and 13% of all participants were…

  1. Benefits and Pitfalls: Simple Guidelines for the Use of Social Networking Tools in K-12 Education

    Science.gov (United States)

    Huffman, Stephanie

    2013-01-01

    The article will outline a framework for the use of social networking tools in K-12 education framed around four thought provoking questions: 1) what are the benefits and pitfalls of using social networking tools in P-12 education, 2) how do we plan effectively for the use of social networking tool, 3) what role does professional development play…

  2. Makerspaces: The Next Iteration for Educational Technology in K-12 Schools

    Science.gov (United States)

    Strycker, Jesse

    2015-01-01

    With the continually growing number of computers and mobile devices available in K-12 schools, the need is dwindling for dedicated computer labs and media centers. Some schools are starting to repurpose those facilities into different kinds of exploratory learning environments known as "makerspaces". This article discusses this next…

  3. Increasing Diversity in K-12 School Leadership. Policy Brief 2018-3

    Science.gov (United States)

    Castro, Andrene; Germain, Emily; Gooden, Mark

    2018-01-01

    Principals represent the most "visible" form of leadership in schools, but current workforce data show that K-12 school principals are overwhelmingly white and fail to reflect the diversity within the student population. With increased policy focus on teacher diversity, equal attention must also be directed towards the lack of diversity…

  4. Manifesting Destiny: Re/Presentations of Indigenous Peoples in K-12 U.S. History Standards

    Science.gov (United States)

    Shear, Sarah B.; Knowles, Ryan T.; Soden, Gregory J.; Castro, Antonio J.

    2015-01-01

    In this mixed-methods study, we use a postcolonial framework to investigate how state standards represent Indigenous histories and cultures. The research questions that guided this study include: (a) What is the frequency of Indigenous content (histories, cultures, current issues) covered in state-level U.S. history standards for K-12? (b) What is…

  5. Modern Rhythmic Gymnastics. A Supplement to the K-12 Physical Education Curriculum Guide. Curriculum Support Series.

    Science.gov (United States)

    Willoughby, Heather; Plumton, Diane

    This resource package has been designed to assist the instructor in using modern rhythmic gymnastics (MRG) to support the objectives cited in the "K-12 Physical Education Curriculum Guide," developed by the Manitoba Department of Education. MRG is based on scientific principles of movement, and makes use of small, hand-held apparatus…

  6. Explaining Technology Integration in K-12 Classrooms: A Multilevel Path Analysis Model

    Science.gov (United States)

    Liu, Feng; Ritzhaupt, Albert D.; Dawson, Kara; Barron, Ann E.

    2017-01-01

    The purpose of this research was to design and test a model of classroom technology integration in the context of K-12 schools. The proposed multilevel path analysis model includes teacher, contextual, and school related variables on a teacher's use of technology and confidence and comfort using technology as mediators of classroom technology…

  7. K-12 Teachers' Perceptions of and Their Satisfaction with Interaction Type in Blended Learning Environments

    Science.gov (United States)

    Kuo, Yu-Chun; Belland, Brian R.; Schroder, Kerstin E. E.; Walker, Andrew E.

    2014-01-01

    Blended learning is an effective approach to instruction that combines features of face-to-face learning and computer-mediated learning. This study investigated the relationship between student perceptions of three types of interaction and blended learning course satisfaction. The participants included K-12 teachers enrolled in a graduate-level…

  8. Arts Education K-12: Teacher Handbook. North Carolina Competency-Based Curriculum Subject-by-Subject.

    Science.gov (United States)

    Chapman, Barbara Holland

    The North Carolina arts education curriculum encompasses K-12 programs in dance, folk arts, music, theater arts, and visual arts. It is designed to provide a scope and sequence which encourages students to develop the essential senses of sight, hearing, smell, taste, touch, and kinetic awareness. It provides opportunities to develop thinking…

  9. Surveying Chinese In-Service K12 Teachers' Technology, Pedagogy, and Content Knowledge

    Science.gov (United States)

    Liu, Qingtang; Zhang, Si; Wang, Qiyun

    2015-01-01

    Technology, pedagogy, and content knowledge (TPACK) has been considered as a promising theoretical framework to guide teacher educators in designing and developing in-service K12 teacher education programs. However, it seems unclear whether in-service teachers have different TPACK perceptions when entering the education programs. This study…

  10. A Professional Learning Program Designed to Increase K-12 Teachers' Instructional Technology Use

    Science.gov (United States)

    Spencer, Lisa A.

    2014-01-01

    Despite the ready availability of many instructional-technology resources, many teachers in the researched Maryland school district are uncomfortable using technology to deliver content. This concurrent mixed methods case study examined the impact of Sharing Technology with Educators Program (STEP) on 269 K-12 teachers' technology use. The study…

  11. Developing a Nationwide K-12 Outreach Model: Physiology Understanding (PhUn) Week 10 Years Later

    Science.gov (United States)

    Stieben, Margaret; Halpin, Patricia A.; Matyas, Marsha Lakes

    2017-01-01

    Since 2005, nearly 600 Physiology Understanding Week (PhUn Week) events have taken place across the U.S., involving American Physiological Society (APS) members in K-12 outreach. The program seeks to build student understanding of physiology and physiology careers, assist teachers in recognizing physiology in their standards-based curriculum, and…

  12. Mobile Apps for Reflection in Learning: A Design Research in K-12 Education

    Science.gov (United States)

    Leinonen, Teemu; Keune, Anna; Veermans, Marjaana; Toikkanen, Tarmo

    2016-01-01

    This study takes a design-based research approach to explore how applications designed for mobile devices could support reflection in learning in K-12 education. Use of mobile devices is increasing in schools. Most of the educational apps support single-person use of interactive learning materials, simulations and learning games. Apps designed to…

  13. Environmental Education and K-12 Student Outcomes: A Review and Analysis of Research

    Science.gov (United States)

    Ardoin, Nicole M.; Bowers, Alison W.; Roth, Noelle Wyman; Holthuis, Nicole

    2018-01-01

    Many practitioners and researchers describe academic and environmental benefits of environmental education for kindergarten through twelfth grade (K-12) students. To consider the empirical underpinnings of those program descriptions, we systematically analyzed the peer-reviewed literature (1994-2013), focusing on outcomes of environmental…

  14. Active Commuting among K-12 Educators: A Study Examining Walking and Biking to Work

    Directory of Open Access Journals (Sweden)

    Melissa Bopp

    2013-01-01

    Full Text Available Background. Walking and biking to work, active commuting (AC is associated with many health benefits, though rates of AC remain low in the US. K-12 educators represent a significant portion of the workforce, and employee health and associated costs may have significant economic impact. Therefore, the purpose of this study was to examine the current rates of AC and factors associated with AC among K-12 educators. Methods. A volunteer sample of K-12 educators ( was recruited to participate in an online survey. Participants responded about AC patterns and social ecological influences on AC (individual, interpersonal, institutional, community, and environmental factors. -tests and ANOVAs examined trends in AC, and Pearson correlations examined the relationship between AC and dependent variables. Multiple regression analysis determined the relative influence of individual, interpersonal, institutional, community, and environmental levels on AC. Results. Participants actively commuted times/week. There were several individual, interpersonal, institutional, community, and environmental factors significantly related to AC. The full model explained 60.8% of the variance in AC behavior. Conclusions. This study provides insight on the factors that determine K-12 educators mode of commute and provide some insight for employee wellness among this population.

  15. The Design, Implementation and Evaluation of Korean K-12 Teacher Training Workshops

    Directory of Open Access Journals (Sweden)

    Sang Yee Cheon

    2017-06-01

    Full Text Available In contrast to public K-12 schools with relatively few Korean language resources, there are about 1,400 Korean community schools in the United States. In most states, K-12 students who are interested in learning about Korean language and culture have no other option but to attend Korean community schools. The purpose of this study is to report on enhanced teacher training workshops for Korean K-12 and community school teachers by seeking a remedy for limitations and problems that previous studies identified. This study will cover the current status of K-12 and Korean community schools in the United States, a summary of a needs analysis of Korean community schools in Hawaii issued in a previous study, the design and implementation of the workshop for Korean language teachers, and the results of the participants’ responses from their exit survey. This report will also include the conclusion of the study, its limitations and implications for future workshops relevant to teachers of other Less Commonly Taught Languages (LCTLs.

  16. Commentary: Mis-Education in K-12 Teaching about Hmong Culture, Identity, History and Religion

    Directory of Open Access Journals (Sweden)

    Kou Yang

    2012-01-01

    Full Text Available This commentary article discusses several examples of inaccurate information about the Hmong presented in contemporary materials produced by school district staff and/or published by mainstream publishers in the United States for use with the K-12 market to teach about Hmong culture and history.

  17. California and the "Common Core": Will There Be a New Debate about K-12 Standards?

    Science.gov (United States)

    EdSource, 2010

    2010-01-01

    A growing chorus of state and federal policymakers, large foundations, and business leaders across the country are calling for states to adopt a common, rigorous body of college- and career-ready skills and knowledge in English and mathematics that all K-12 students will be expected to master by the time they graduate. This report looks at the…

  18. The Cost Burden to Minnesota K-12 when Children Are Unprepared for Kindergarten. [Summary

    Science.gov (United States)

    Chase, Richard; Coffee-Borden, Brandon; Anton, Paul; Moore, Christopher; Valorose, Jennifer

    2008-01-01

    This summary presents highlights of "The Cost Burden to Minnesota K-12 when Children Are Unprepared for Kindergarten" [ED511612]. A number of studies document the long-term public and societal benefits of early childhood education, including the reduced costs associated with child welfare, public assistance, crime and incarceration, and…

  19. Crossing the Bridge: Transitioning from a K-12 Teacher to a College Professor

    Science.gov (United States)

    Page, Steven; Jenks, Charles

    2012-01-01

    This is a qualitative study that was conducted to gain a better understanding of the experiences of professors in Colleges of Education who were former K-12 teachers. The study presents the responses of eighty-nine professors from across the United States. Coding based on the university setting (national, large regional, small regional) in which…

  20. An Evaluation of the Conditions, Processes, and Consequences of Laptop Computing in K-12 Classrooms

    Science.gov (United States)

    Cavanaugh, Cathy; Dawson, Kara; Ritzhaupt, Albert

    2011-01-01

    This article examines how laptop computing technology, teacher professional development, and systematic support resulted in changed teaching practices and increased student achievement in 47 K-12 schools in 11 Florida school districts. The overview of a large-scale study documents the type and magnitude of change in student-centered teaching,…

  1. Laptops in the K-12 Classrooms: Exploring Factors Impacting Instructional Use

    Science.gov (United States)

    Inan, Fethi A.; Lowther, Deborah L.

    2010-01-01

    The purpose of this study was to examine factors affecting teachers' integration of laptops into classroom instruction. A research-based path model was tested based on data gathered from 379 K-12 school teachers to examine direct and indirect contributions of relevant institutional factors (overall support for school technology, technical support,…

  2. A Case Study of Rural New Mexico K-12 Teachers' Perceptions of Standardized Testing

    Science.gov (United States)

    Hite-Pope, Kim

    2017-01-01

    The purpose of this paper was to examine K-12 teachers' classroom experiences with standardized testing in rural New Mexico schools. Standardized tests have significantly changed the landscape of education with the use of students' test scores as a determining factor for advancement or failure for teachers (Simpson, Lacava, & Graner, 2013).…

  3. A Field Study of Telepractice for School Intervention Using the ASHA NOMS K-12 Database

    Science.gov (United States)

    Gabel, Rodney; Grogan-Johnson, Sue; Alvares, Robin; Bechstein, Leah; Taylor, Jacquelyn

    2013-01-01

    The purpose of this article is to describe the characteristics and effectiveness of a telepractice speech-language therapy program for school-age children. Outcome data related to the caseload, type and amount of intervention, and student progress from a school-based telepractice therapy program were compared with the K-12 Schools National…

  4. Teaching and Learning with Mobile Computing Devices: Case Study in K-12 Classrooms

    Science.gov (United States)

    Grant, Michael M.; Tamim, Suha; Brown, Dorian B.; Sweeney, Joseph P.; Ferguson, Fatima K.; Jones, Lakavious B.

    2015-01-01

    While ownership of mobile computing devices, such as cellphones, smartphones, and tablet computers, has been rapid, the adoption of these devices in K-12 classrooms has been measured. Some schools and individual teachers have integrated mobile devices to support teaching and learning. The purpose of this qualitative research was to describe the…

  5. How Do K-12 Students' Manage Applications on Their Mobile Devices?

    Science.gov (United States)

    Aladjem, Ruthi; Hardof, Sharon

    2016-01-01

    Personal information management (PIM) is a research field that examines the activities by which users save, organize and retrieve personal information items. PIM is a one of the essential new literacies for learners in the 21st century. This paper reports results from a pilot study that explored PIM practices and strategies of K-12 students, on…

  6. K-12 Student Use of Web 2.0 Tools: A Global Study

    Science.gov (United States)

    Toledo, Cheri; Shepard, MaryFriend

    2011-01-01

    Over the past decade, Internet use has increased 445% worldwide. This boom has enabled widespread access to online tools and digital spaces for educational practices. The results of this study of Web 2.0 tool use in kindergarten through high school (K-12) classrooms around the world will be presented. A web-based survey was sent out through online…

  7. Calibration of the AG23K-12.5 Feed Horn

    DEFF Research Database (Denmark)

    Pivnenko, Sergey; Breinbjerg, Olav

    This report documents the calibration measurement of the dual-linearly polarized AG23K-12.5 feed horn. The measurement comprises on-axis gain, on-axis polarization characteristics, and input reflection coefficient at 701 frequencies in the frequency range from 9.0-16.0 GHz. The measurement...

  8. Immigration and Education: What Should K-12 Teachers, School Administrators, and Staff Know?

    Science.gov (United States)

    Rubinstein-Avila, Eliane

    2017-01-01

    We are currently living in an era of mass global migration. Therefore, it is a pertinent time to reflect on the challenges and the possibilities inherent in educating immigrant and refugee children. Because of the importance immigration has played in the history of the United States, it may be assumed that American K-12 teachers and school…

  9. Perceptions and Experiences of K-12 Educational Leaders in Response to the 27 April 2011 Tornadoes

    Science.gov (United States)

    Bishop, William E.; Fifolt, Matthew; Peters, Gary B.; Gurley, D. Keith; Collins, Loucrecia

    2015-01-01

    The purpose of this phenomenological study was to capture first-hand accounts of K-12 educational leaders whose school districts were directly affected by the deadly 27 April 2011 tornadoes in rural Alabama, USA. This study was framed by the literature base of leadership; specifically crisis leadership and resilience theory. Findings are organised…

  10. Learning Analysis of K-12 Students' Online Problem Solving: A Three-Stage Assessment Approach

    Science.gov (United States)

    Hu, Yiling; Wu, Bian; Gu, Xiaoqing

    2017-01-01

    Problem solving is considered a fundamental human skill. However, large-scale assessment of problem solving in K-12 education remains a challenging task. Researchers have argued for the development of an enhanced assessment approach through joint effort from multiple disciplines. In this study, a three-stage approach based on an evidence-centered…

  11. Reconsidering Genre Theory in K-12 Schools: A Response to School Reforms in the United States

    Science.gov (United States)

    Gebhard, Meg; Harman, Ruth

    2011-01-01

    Education reforms in the United States have placed new demands on English language learners (ELLs) and their teachers in K-12 public schools. In response, many teachers, teacher educators, and literacy scholars are reexamining genre theory and genre-based pedagogy as a way of supporting the academic literacy development of the growing number of…

  12. Comparing Cross-Cultural Multicultural Self-Awareness among K-12 In-Service School Teachers

    Science.gov (United States)

    Koyama, Chieko; Plash, Shawn; Davis, Kirk

    2012-01-01

    The present study explored multicultural self-awareness among 134 K-12 in-service school teachers using the Cultural Diversity Awareness Inventory (CDAI). The results were compared to Yeung's (2006), allowing for a comparison between Eastern and Western cultures. A composite score was generated for each of the five areas measured by the CDAI. A…

  13. Development of Design Guidance for K-12 Schools from 30% to 50% Energy Savings: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Pless, S.; Torcellini, P.; Long, N.

    2008-07-01

    This paper describes the development of energy efficiency recommendations for achieving 30% whole-building energy savings in K-12 schools over levels achieved by following the ANSI/ASHRAE/IESNA Standard 90.1. These design recommendations look at building envelope, fenestration, lighting systems (including electrical lights and daylighting), HVAC systems, building automation and controls, outside air treatment, and service water heating.

  14. Single-Subject Designs and Action Research in the K-12 Setting

    Science.gov (United States)

    Forbes, Sean A.; Ross, Margaret E.; Chesser, Svetlana S.

    2011-01-01

    In as much as educational research is concerned with individual student assessment and development, it is surprising that single-subject designs are not more readily utilized in classroom-based action research. The purpose of this article is to emphasize benefits of single-subject research in the K-12 setting, given that teachers teach and assess…

  15. Leading by Following: An Analysis of How K-12 School Leaders Use Twitter

    Science.gov (United States)

    Sauers, Nicholas J.; Richardson, Jayson W.

    2015-01-01

    This study analyzed how active Twitter users who are also school leaders used the tool. The researchers collaboratively identified K-12 school leaders who were active on Twitter and then collected tweets from those school leaders. The final sample for this study included 115 Twitter users and over 180,000 tweets from those individuals. The results…

  16. Empowering Educators through Teacher Research: Promoting Qualitative Inquiry among K-12 Educators

    Science.gov (United States)

    Clarke, E. Jason

    2012-01-01

    The desire to find pedagogically effective uses of technology in K-12 education has exposed the need for reliable professional development programs that empower teachers to identify the problems and needs they have in their classrooms, apply a process of systematic inquiry in order to discover solutions to those problems, and to share those…

  17. How to Implement Rigorous Computer Science Education in K-12 Schools? Some Answers and Many Questions

    Science.gov (United States)

    Hubwieser, Peter; Armoni, Michal; Giannakos, Michail N.

    2015-01-01

    Aiming to collect various concepts, approaches, and strategies for improving computer science education in K-12 schools, we edited this second special issue of the "ACM TOCE" journal. Our intention was to collect a set of case studies from different countries that would describe all relevant aspects of specific implementations of…

  18. iPads in K-12 Schools: A Grounded Theory Study of Value

    Science.gov (United States)

    Townsend, Mary Beth

    2017-01-01

    This qualitative grounded theory study investigated the value of iPads in K-12 schools when used in one-to-one ratios. The purpose of the study was to understand the perspectives of teachers using iPads in one-to-one ratios for teaching and learning in the classroom and administrators responsible for the implementation of these devices. The…

  19. The Preparation of Teacher Candidates for K-12 Online Learning Environments: A Case Study

    Science.gov (United States)

    Williams, Nicole V.

    2015-01-01

    The purpose of this study was to determine how teacher education programs may better prepare teacher candidates to teach in K-12 online learning environments. The primary research question addressed was: What specific knowledge, skills, and dispositions should teacher education programs include in their curriculum to better prepare teacher…

  20. Teacher Certification of American Sign Language Faculty at K-12 and Higher Education Institutions

    Science.gov (United States)

    Fox, Ashley Leann Chance

    2010-01-01

    American Sign Language (ASL) is ranked fourth among heritage languages taken by students in the United States. The number of ASL classes offered at the K-12 and Institutions of Higher Education are on the rise, yet the number of certified ASL teachers remains stagnant. This study examines the reasons why American Sign Language teachers choose to…

  1. The Debate of Evolution versus Intelligent Design: Is Critical Thinking Occurring among K-12 Students?

    Science.gov (United States)

    Hoodman, Kyle Nathan

    2010-01-01

    This study investigates how evolution versus intelligent design is handled in the public, private Christian, private Jewish, and Christian Home-school K-12 settings through a review of the current literature and by interviewing teachers in these educational venues. Fourteen public, private, and homeschool educators responded to an interview…

  2. Peer Mentoring and Peer Tutoring among K-12 Students: A Literature Review

    Science.gov (United States)

    Goodrich, Andrew

    2018-01-01

    The purpose of this literature review is to examine research on peer mentoring among K-12 students to assist practitioners with how to incorporate these instructional techniques into their own music programs. Primary themes across the music education literature of peer mentoring include the role of music teachers, the role of students as they…

  3. Cisco Networking Academy: Next-Generation Assessments and Their Implications for K-12 Education

    Science.gov (United States)

    Liu, Meredith

    2014-01-01

    To illuminate the possibilities for next-generation assessments in K-12 schools, this case study profiles the Cisco Networking Academy, which creates comprehensive online training curriculum to teach networking skills. Since 1997, the Cisco Networking Academy has served more than five million high school and college students and now delivers…

  4. Outstanding Science Trade Books for Students K-12: Books Published in 2015

    Science.gov (United States)

    Science and Children, 2016

    2016-01-01

    Science teachers and mentors continue to be challenged to meet the high expectations of "A Framework for K-12 Science Education" and the "Next Generation Science Standards" ("NGSS"). Indeed the "Framework" urges to help learners "[build] progressively more sophisticated explanations of natural…

  5. Trends in Technology Planning and Funding in Florida K-12 Public Schools

    Science.gov (United States)

    Ritzhaupt, Albert Dieter; Hohlfeld, Tina N; Barron, Ann E.; Kemker, Kate

    2008-01-01

    This empirical research investigates trends in technology planning and funding in Florida's K-12 public schools between the 2003-04 and 2005-06 academic years. Survey items that focused on funding and planning issues on Florida's statewide school technology integration survey were analyzed using logistic models. Results indicate a significant…

  6. Networking K-12 Schools: Architecture Models and Evaluation of Costs and Benefits.

    Science.gov (United States)

    Rothstein, Russell Isaac

    This thesis examines the cost and benefits of communication networks in K-12 schools using cost analysis of five technology models with increasing levels of connectivity. Data indicate that the cost of the network hardware is only a small fraction of the overall networking costs. PC purchases, initial training, and retrofitting are the largest…

  7. Identifying and Reconstructing Common Cold Misconceptions among Developing K-12 Educators

    Science.gov (United States)

    Johnson, Marcus Lee; Bungum, Timothy

    2013-01-01

    Background: Common cold misconceptions may contribute to ill-informed decisions and recommendations made by K-12 educators who often encounter infected students. Understanding the structure of educators' misconceptions can be used to improve health instruction in teacher professional preparation programs. Purpose: The purposes of this project were…

  8. Engineering Design Skills Coverage in K-12 Engineering Program Curriculum Materials in the USA

    Science.gov (United States)

    Chabalengula, Vivien M.; Mumba, Frackson

    2017-01-01

    The current "K-12 Science Education framework" and "Next Generation Science Standards" (NGSS) in the United States emphasise the integration of engineering design in science instruction to promote scientific literacy and engineering design skills among students. As such, many engineering education programmes have developed…

  9. The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner

    Science.gov (United States)

    Kondrashov, F. A.; Toshchakov, S. V.; Dominova, I.; Shvyreva, U. S.; Vrublevskaya, V. V.; Morenkov, O. S.; Panyukov, V. V.

    2017-01-01

    Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase

  10. The SERC K12 Educators Portal to Teaching Activities and Pedagogic Approaches

    Science.gov (United States)

    Larsen, K.; Kirk, K. B.; Manduca, C. A.; Ledley, T. S.; Schmitt, L.

    2013-12-01

    The Science Education Resource Center (SERC) has created a portal to information for K12 educators to provide high-quality grade level appropriate materials from a wide variety of projects and topics. These materials were compiled across the SERC site, showcasing materials that were created for, or easily adaptable to, K12 classrooms. This resource will help support implementation of Next Generation Science Standards by assisting educators in finding innovative resources to address areas of instruction that are conceptually different than previous national and state science standards. Specifically, the K12 portal assists educators in learning about approaches that address the cross-cutting nature of science concepts, increasing students quantitative reasoning and numeracy skills, incorporating technology such as GIS in the classroom, and by assisting educators of all levels of K12 instruction in using relevant and meaningful ways to teach science concepts. The K12 portal supports educators by providing access to hundreds of teaching activities covering a wide array of science topics and grade levels many of which have been rigorously reviewed for pedagogic quality and scientific accuracy. The portal also provides access to web pages that enhance teaching practices that help increase student's system thinking skills, make lectures interactive, assist instructors in conducting safe and effective indoor and outdoor labs, providing support for teaching energy and climate literacy principles, assisting educators in addressing controversial content, provide guidance in engaging students affective domain, and provides a collection of tools for making teaching relevant in 21st century classrooms including using GIS, Google Earth, videos, visualizations and simulations to model and describe scientific concepts. The portal also provides access to material for specific content and audiences by (1) Supporting AGIs 'Map your World' week to specifically highlight teaching

  11. Isolation and Antibiotics Susceptibility Patterns of Escherichia Coli ...

    African Journals Online (AJOL)

    Escherichia coli 0157.H7 were confirmed serologically using latex agglutination kits (OxoidR UK). The isolates were tested for susceptibility to five commonly used antimicrobial agents and plasmid transfer was also carried out using E. coli K12 356 recipient. Out of the 61 non-Sorbitol fermenting (NSF) E. coli isolated from ...

  12. Preparing Teacher Candidates for Virtual Field Placements via an Exposure to K-12 Online Teaching

    Directory of Open Access Journals (Sweden)

    Tian Luo

    2016-12-01

    Full Text Available Aim/Purpose\tThe goal of this project was to determine what effects exposure to online K-12 teaching and learning activities had on teacher candidates’ perceptions of K-12 online learning, how the exposure allowed teacher candidates to reach greater understanding of online pedagogy, and what effect such exposure had on teacher candidates’ aspirations to complete virtual field experiences. Background\tWith an increasing number of K-12 students learning online within full-time online schools and in blended learning environments, universities must prepare future educators to teach in virtual environments including clinical practice. Before engaging in online field placement, preservice teachers must be oriented to online K-12 teaching and learning. Methodology\tUsing a design-based, mixed-method research methodology, this study drew samples from four sections of a hybrid technology integration course. Preservice teachers’ papers detailing their perceptions, focus groups, and surveys were used to gauge changes in perceptions of online learning after participating in online teaching and learning activities. Contribution\tThe study demonstrated that an exposure to online K-12 classrooms stimulated preservice teachers’ interest in online teaching as they began to feel that online education could be equivalent to traditional education. Findings\tStudents’ perceptions positively improved the equivalency of online learning to traditional schooling, the possibility of positive relationships between teachers and students, and the ability to create interactive learning. Students also reported being more knowledgeable and showed increased interest in participating in virtual field experiences. Future Research\tFuture research may continue to examine if the exposure course, combined with a short-term clinical experiences and long-term online apprenticeships may serve to prepare graduates with the skills necessary to teach in classrooms of the future.

  13. Females and STEM: Determining the K-12 Experiences that Influenced Women to Pursue STEM Fields

    Science.gov (United States)

    Petersen, Anne Marie

    In the United States, careers in the fields of Science, Technology, Engineering, and Mathematics (STEM) are increasing yet there are not enough trained personnel to meet this demand. In addition, of those that seek to pursue STEM fields in the United States, only 26% are female. In order to increase the number of women seeking STEM based bachelor's degrees, K-12 education must provide a foundation that prepares students for entry into these fields. The purpose of this phenomenological study was to determine the perceived K-12 experiences that influenced females to pursue a STEM field. Twelve college juniors or seniors seeking a degree in Biology, Mathematics, or Physics were interviewed concerning their K-12 experiences. These interviews were analyzed and six themes emerged. Teacher passion and classroom characteristics such as incorporating challenging activities played a significant role in the females' decisions to enter STEM fields. Extra-curricular activities such as volunteer and mentor opportunities and the females' need to benefit others also influenced females in their career choice. Both the formal (within the school) and informal (outside of the traditional classroom) pipeline opportunities that these students encountered helped develop a sense of self-efficacy in science and mathematics; this self-efficacy enabled them to persist in pursuing these career fields. Several participants cited barriers that they encountered in K-12 education, but these barriers were primarily internal as they struggled with overcoming self-imposed obstacles in learning and being competitive in the mathematics and science classrooms. The experiences from these female students can be used by K-12 educators to prepare and encourage current female students to enter STEM occupations.

  14. Collagen-like proteins in pathogenic E. coli strains.

    Directory of Open Access Journals (Sweden)

    Neelanjana Ghosh

    Full Text Available The genome sequences of enterohaemorrhagic E. coli O157:H7 strains show multiple open-reading frames with collagen-like sequences that are absent from the common laboratory strain K-12. These putative collagens are included in prophages embedded in O157:H7 genomes. These prophages carry numerous genes related to strain virulence and have been shown to be inducible and capable of disseminating virulence factors by horizontal gene transfer. We have cloned two collagen-like proteins from E. coli O157:H7 into a laboratory strain and analysed the structure and conformation of the recombinant proteins and several of their constituting domains by a variety of spectroscopic, biophysical, and electron microscopy techniques. We show that these molecules exhibit many of the characteristics of vertebrate collagens, including trimer formation and the presence of a collagen triple helical domain. They also contain a C-terminal trimerization domain, and a trimeric α-helical coiled-coil domain with an unusual amino acid sequence almost completely lacking leucine, valine or isoleucine residues. Intriguingly, these molecules show high thermal stability, with the collagen domain being more stable than those of vertebrate fibrillar collagens, which are much longer and post-translationally modified. Under the electron microscope, collagen-like proteins from E. coli O157:H7 show a dumbbell shape, with two globular domains joined by a hinged stalk. This morphology is consistent with their likely role as trimeric phage side-tail proteins that participate in the attachment of phage particles to E. coli target cells, either directly or through assembly with other phage tail proteins. Thus, collagen-like proteins in enterohaemorrhagic E. coli genomes may have a direct role in the dissemination of virulence-related genes through infection of harmless strains by induced bacteriophages.

  15. Whole-genome sequencing and genetic analysis reveals novel stress responses against individual constituents of essential oils in Escherichia coli.

    Science.gov (United States)

    Chueca, Beatriz; Renzoni, Adriana; Berdejo, Daniel; Pagán, Rafael; Kelley, William L; García-Gonzalo, Diego

    2018-01-26

    Food preservation by the use of essential oils (EOs) is being extensively studied, because of the antimicrobial properties of their individual constituents (ICs). Three resistant mutants (termed CAR, CIT and LIM) of Escherichia coli MG1655 were selected by subculturing with the ICs carvacrol, citral and (+)-limonene oxide, respectively. These derivative strains showed increased MIC values to ICs and concomitant enhanced resistance to various antibiotics (ampicillin, trimethoprim, chloramphenicol, tetracycline, kanamycin, novobiocin, norfloxacin, cephalexin and nalidixic acid) compared with the parental strain (WT).Whole genome sequencing (WGS) of these hyper-resistant strains permitted the identification of single nucleotide polymorphisms (SNPs) and deletions in comparison with WT.In order to analyze the contribution of these mutations to the increased antimicrobial resistance detected in hyper-resistant strains, derivative strains were constructed by allelic reversion. A role of SoxR D137Y missense mutation in CAR was confirmed in growth under the presence of some ICs and antibiotics, and in its tolerance to ICs, but not to heat lethal treatments. In CIT, increased resistance relied on a contribution between several detected SNPs resulting in a frameshift in MarR and an in-frame GyrB ΔG157 mutation. Finally, both the insertion resulting in an AcrR frameshift and large chromosomal deletions found in LIM, correlated with the hyper-resistant phenotype of this strain. The nature of the obtained mutants suggests intriguing links to cellular defense mechanisms previously implicated in antibiotic resistance.IMPORTANCE The antimicrobial efficacy of ICs has been proven over the years together with their potential to improve traditional heat treatments by reducing treatment intensity and consequently adverse effects on food quality. However, the mechanisms of bacterial inactivation by ICs are still not well understood, in contrast to antibiotics. We performed WGS of three

  16. Gene Expression Analysis of Escherichia Coli Grown in Miniaturized Bioreactor Platforms for High-Throughput Analysis of Growth and genomic Data

    DEFF Research Database (Denmark)

    Boccazzi, P.; Zanzotto, A.; Szita, Nicolas

    2005-01-01

    Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturized....... In general, these changes in gene expression levels were similar to those observed in 1,000-fold larger cultures. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for investigating these organisms. Our results from microscale...... cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies....

  17. Genomic comparison of Escherichia coli serotype O103:H2 isolates with and without verotoxin genes: implications for risk assessment of strains commonly found in ruminant reservoirs

    Directory of Open Access Journals (Sweden)

    Robert Söderlund

    2016-02-01

    Full Text Available Introduction: Escherichia coli O103:H2 occurs as verotoxigenic E. coli (VTEC carrying only vtx1 or vtx2 or both variants, but also as vtx-negative atypical enteropathogenic E. coli (aEPEC. The majority of E. coli O103:H2 identified from cases of human disease are caused by the VTEC form. If aEPEC strains frequently acquire verotoxin genes and become VTEC, they must be considered a significant public health concern. In this study, we have characterized and compared aEPEC and VTEC isolates of E. coli O103:H2 from Swedish cattle. Methods: Fourteen isolates of E. coli O103:H2 with and without verotoxin genes were collected from samples of cattle feces taken during a nationwide cattle prevalence study 2011–2012. Isolates were sequenced with a 2×100 bp setup on a HiSeq2500 instrument producing >100× coverage per isolate. Single-nucleotide polymorphism (SNP typing was performed using the genome analysis tool kit (GATK. Virulence genes and other regions of interest were detected. Susceptibility to transduction by two verotoxin-encoding phages was investigated for one representative aEPEC O103:H2 isolate. Results and Discussion: This study shows that aEPEC O103:H2 is more commonly found (64% than VTEC O103:H2 (36% in the Swedish cattle reservoir. The only verotoxin gene variant identified was vtx1a. Phylogenetic comparison by SNP analysis indicates that while certain subgroups of aEPEC and VTEC are closely related and have otherwise near identical virulence gene repertoires, they belong to separate lineages. This indicates that the uptake or loss of verotoxin genes is a rare event in the natural cattle environment of these bacteria. However, a representative of a VTEC-like aEPEC O103:H2 subgroup could be stably lysogenized by a vtx-encoding phage in vitro.

  18. QnrS1- and Aac(6’-Ib-cr-producing Escherichia coli among isolates from animals of different sources: susceptibility and genomic characterization

    Directory of Open Access Journals (Sweden)

    Daniela eJones-Dias

    2016-05-01

    Full Text Available Salmonella enterica and Escherichia coli can inhabit humans and animals from multiple origins. These bacteria are often associated with gastroenteritis in animals, being a frequent cause of resistant zoonotic infections. In fact, bacteria from animals can be transmitted to humans through the food chain and direct contact. In this study, we aimed to assess the antibiotic susceptibility of a collection of S. enterica and E. coli recovered from animals of different sources, performing a genomic comparison of the plasmid-mediated quinolone resistance (PMQR-producing isolates detected.Antibiotic susceptibility testing revealed a high number of non wild-type isolates for fluoroquinolones among S. enterica recovered from poultry isolates. In turn, the frequency of non-wild-type E. coli to nalidixic acid and ciprofloxacin was higher in food-producing animals than in companion or zoo animals. Globally, we detected two qnrS1 and two aac(6’-Ib-cr in E. coli isolates recovered from animals of different origins. The genomic characterization of QnrS1-producing E. coli showed high genomic similarity (O86:H12 and ST2297, although they have been recovered from a healthy turtle dove from a Zoo Park, and from a dog showing symptoms of infection. The qnrS1 gene was encoded in a IncN plasmid, also carrying blaTEM-1-containing Tn3. Isolates harboring aac(6’-Ib-cr were detected in two captive bottlenose dolphins, within a time span of two years. The additional antibiotic resistance genes of the two aac(6’-Ib-cr-positive isolates (blaOXA-1, blaTEM-1, blaCTX-M-15, catB3, aac(3-IIa and tetA were enclosed in IncFIA plasmids that differed in a single transposase and 60 single nucleotide variants. The isolates could be assigned to the same genetic sublineage – ST131 fimH30-Rx (O25:H4, confirming clonal spread. PMQR-producing isolates were associated with symptomatic and asymptomatic hosts, which highlight the aptitude of E. coli to act as silent vehicles, allowing

  19. Issues Related to Technology in Teacher Education Programs and K-12 Public Schools in Texas

    Directory of Open Access Journals (Sweden)

    Jon Denton

    1999-01-01

    Full Text Available This paper describes the support systems, financial support, current use of technology, and infrastructure issues at selected institutions of higher education (IHE and in K-12 public schools in the State of Texas, United States. Discussion is provided on how current practitioners in public schools and institutions of higher education that prepare pre-service teachers for these schools match regarding technology. In depth discussion is provided on two surveys--one of higher education institutions and one of public schools--along with a discussion of the findings as they relate to the ability of institutions of higher education to support K-12 schools through the preparation of future teachers well equipped to use and comfortable with current and emerging technologies.

  20. Advanced Energy Design Guide K-12: Next Generation of School Design and Operation

    Energy Technology Data Exchange (ETDEWEB)

    Torcellini, Paul A [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pless, Shanti [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-01-01

    Driven by energy efficiency advances and renewable energy cost reductions, zero energy buildings are popping up all around the country. Although zero energy represents a bold paradigm shift - from buildings that consume energy to buildings that produce enough energy to meet their energy needs on an annual basis - it isn't a sudden shift. Zero energy buildings are the result of steady, incremental progress by researchers and building professionals working together to improve building energy performance. ASHRAE is taking the lead by publishing - in partnership with the American Institute of Architects (AIA), the Illuminating Engineering Society (IES), the U.S. Green Building Council (USGBC), and the U.S. Department of Energy (DOE) - a new series of advanced energy design guides (AEDGs) focused on zero energy buildings. The recently completed Advanced Energy Design Guide for K-12 School Buildings: Achieving Zero Energy (K-12 ZE AEDG) is the first in this series.

  1. Graduate students' motivation to teach plant sciences to K-12 audiences

    OpenAIRE

    Welsh, Melissa Leiden

    2014-01-01

    Graduate students' motivation to share their knowledge and research with K-12 audiences as future scientists is informed by their beliefs and perceived value of science literacy outreach. Graduate training programs in academia integrate outreach teaching components to equip future scientists with a variety of communication skills, which may reflect either a transmission of knowledge to the learner or through engagement with the learner. As such, the education component of the "Partnership for...

  2. Multi-Directional Microaggressions: Filipino Students and Everyday Racism in Hawai`i's K-12 Schools

    OpenAIRE

    Viernes, Kate

    2014-01-01

    This thesis examines Filipino Americans, Hawai`i's largest Asian Pacific Islander (API) group and their experiences with racism in Hawai`i, specifically in its K-12 educational system. Perceptions of Hawai`i as a model of "multiculturalism" obscure how the state's racially diverse population lives in the condition of settler colonialism which reproduce processes of racialization enabled by the islands' white colonizers. Through Critical Race Theory (CRT), I document how racial microaggression...

  3. CESAME: Providing High Quality Professional Development in Science and Mathematics for K-12 Teachers

    Science.gov (United States)

    Hickman, Paul

    2002-04-01

    It is appropriate that after almost half a century of Science and Mathematics education reform we take a look back and a peek forward to understand the present state of this wonderfully complex system. Each of the components of this system including teaching, professional development, assessment, content and the district K-12 curriculum all need to work together if we hope to provide quality science, mathematics and technology education for ALL students. How do the state and national standards drive the system? How do state policies on student testing and teacher licensure come into play? How do we improve the preparation, retention and job satisfaction of our K-12 teachers? What initiatives have made or are making a difference? What else needs to be done? What can the physics community do to support local efforts? This job is too big for any single organization or individual but we each can contribute to the effort. Our Center at Northeastern University, with support from the National Science Foundation, has a sharply defined focus: to get high quality, research-based instructional materials into the hands of K-12 classroom teachers and provide the support they need to use the materials effectively in their classrooms.

  4. Advanced Energy Retrofit Guide: Practical Ways to Improve Energy Performance, K-12 Schools (Book)

    Energy Technology Data Exchange (ETDEWEB)

    2013-12-01

    The U.S. Department of Energy developed the Advanced Energy Retrofit Guides (AERGs) to provide specific methodologies, information, and guidance to help energy managers and other stakeholders plan and execute energy efficiency improvements. Detailed technical discussion is fairly limited. Instead, we emphasize actionable information, practical methodologies, diverse case studies, and unbiased evaluations of the most promising retrofit energy efficiency measures for each building type. A series of AERGs is under development, addressing key segments of the commercial building stock. K-12 schools were selected as one of the highest priority building sectors, because schools affect the lives of most Americans. They also represent approximately 8% of the energy use and 10% of the floor area in commercial buildings nationwide. U.S. K-12 school districts spend more than $8 billion each year on energy - more than they spend on computers and textbooks combined. Most occupy older buildings that often have poor operational performance - more than 30% of schools were built before 1960. The average age of a school is about 42 years - which is nearly the expected serviceable lifespan of the building. K-12 schools offer unique opportunities for deep, cost-effective energy efficiency improvements, and this guide provides convenient and practical guidance for exploiting these opportunities in the context of public, private, and parochial schools.

  5. An Early Start in Robotics – K-12 Case-Study

    Directory of Open Access Journals (Sweden)

    Celina Pinto Leão

    2011-04-01

    Full Text Available

    This paper describes a study carried out with K-12 students. This study is focused on understanding the motivation of these students on the use of robots in the Project Area curricular unit and to understand whether they want to continue their studies in technology areas. K-12 students participated in the RoboParty® event, where the main task is to assemble and program a robot. In other words, the students, in a simple and entertaining way and guided by qualified tutors, learned how to build a robot. At the end of the academic year, a questionnaire was applied to identify and evaluate the K-12 students' opinions regarding the experience. The students’ reaction to this experience as well to the direct contact with the university environment was quite positive.

  6. Using Scientific Visualizations to Enhance Scientific Thinking In K-12 Geoscience Education

    Science.gov (United States)

    Robeck, E.

    2016-12-01

    The same scientific visualizations, animations, and images that are powerful tools for geoscientists can serve an important role in K-12 geoscience education by encouraging students to communicate in ways that help them develop habits of thought that are similar to those used by scientists. Resources such as those created by NASA's Scientific Visualization Studio (SVS), which are intended to inform researchers and the public about NASA missions, can be used in classrooms to promote thoughtful, engaged learning. Instructional materials that make use of those visualizations have been developed and are being used in K-12 classrooms in ways that demonstrate the vitality of the geosciences. For example, the Center for Geoscience and Society at the American Geosciences Institute (AGI) helped to develop a publication that outlines an inquiry-based approach to introducing students to the interpretation of scientific visualizations, even when they have had little to no prior experience with such media. To facilitate these uses, the SVS team worked with Center staff and others to adapt the visualizations, primarily by removing most of the labels and annotations. Engaging with these visually compelling resources serves as an invitation for students to ask questions, interpret data, draw conclusions, and make use of other processes that are key components of scientific thought. This presentation will share specific resources for K-12 teaching (all of which are available online, from NASA, and/or from AGI), as well as the instructional principles that they incorporate.

  7. Opinions on computing education in Korean K-12 system: higher education perspective

    Science.gov (United States)

    Kim, Dae-Kyoo; Jeong, Dongwon; Lu, Lunjin; Debnath, Debatosh; Ming, Hua

    2015-10-01

    The need for computing education in the K-12 curriculum has grown globally. The Republic of Korea is not an exception. In response to the need, the Korean Ministry of Education has announced an outline for software-centric computing education in the K-12 system, which aims at enhancing the current computing education with software emphasis. In this paper, we review the outline from a higher education perspective and provide insights into its constructive improvement based on our experience in computer science education in higher education and a study of global initiatives on computing education. We also consider the social environment for computing education in Korea. In the proposed implementation, we first discuss goals for software-centric computing education and identify areas of focus. The identified areas are discussed in terms of topics to be covered and appropriate exposure of knowledge depth in the three levels in the Korean K-12 system. We then discuss necessary preparations for the success of the plan from academic, governmental and social perspectives.

  8. Draft genome sequences of two fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST90 (ST23 complex) isolated from a calf and a dairy cow in South America.

    Science.gov (United States)

    Sartori, Luciana; Fernandes, Miriam R; Ienne, Susan; de Souza, Tiago A; Gregory, Lilian; Cerdeira, Louise; Lincopan, Nilton

    2017-12-01

    Farm animals have been recognised as important carriers and reservoirs of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. The aim of this study was to report the draft genome sequences of two multidrug-resistant (MDR) CTX-M-15-producing E. coli strains (47VL and 13B) isolated from different bovine hosts (a calf and a dairy cow), housed separately in a commercial dairy farm in Brazil. Total genomic DNA of the E. coli isolates was sequenced using an Illumina MiSeq paired-end 300-bp sequencing platform. Sequence reads were de novo assembled using the A5-miseq pipeline and polishing assembly in Geneious v.R9. The NCBI Prokaryotic Genome Annotation Pipeline v.3.2 was used for genome annotation, whereas whole-genome sequences were analysed using bioinformatic tools from the Center of Genomic Epidemiology and EnteroBase. E. coli 47VL generated a total of 3238770 and E. coli 13B a total of 1422808 paired-end reads of ca. 190× and ca. 80×, respectively. The resistome revealed that both isolates carried resistance genes to aminoglycosides, β-lactams, macrolides, sulphonamides, trimethoprim and tetracycline. Comparative analyses revealed clonal relatedness. In fact, both isolates belonged to sequence type ST90 (clonal complex CC23) and phylogroup AxB1. To our knowledge, these are the first draft genome sequences of CTX-M-15-producing E. coli ST90 isolated from bovines in South America. These data can be used to elucidate genetic features that contribute to colonisation and adaptation of CTX-M-15-producing E. coli in dairy cattle. Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

  9. Genome assembly of E. coli KV7, a BLA-CTX-containing strain isolated from a pig

    NARCIS (Netherlands)

    Bateman, Michael D.; Vries, de S.P.W.; Gupta, Srishti; Guardabassi, Luca; Cavaco, Lina M.; Grant, Andrew J.; Holmes, Mark A.

    1800-01-01

    We report the chromosome and plasmid sequences of a spontaneous nalidixic acid resistant derivative of the ESBL-producing E. coli strain KV7. E. coli KV7 was originally isolated from a healthy pig that was treated prophylactically with ceftiofur. KV7 belongs to serotype O27 and phylogenetic group D,

  10. Characterization of high-level expression and sequencing of the Escherichia coli K-12 cynS gene encoding cyanase.

    OpenAIRE

    Sung, Y C; Anderson, P M; Fuchs, J A

    1987-01-01

    Restriction fragments containing the gene encoding cyanase, cynS, without its transcriptional regulatory sequences were placed downstream of lac and tac promoters in various pUC derivatives to maximize production of cyanase. Plasmid pSJ105, which contains the cynS gene and an upstream open reading frame, gave the highest expression of cyanase. Approximately 50% of the total soluble protein in stationary-phase cultures of a lac-deleted strain containing plasmid pSJ105 was cyanase. The inserted...

  11. Comparative Genomics of an IncA/C Multidrug Resistance Plasmid from Escherichia coli and Klebsiella Isolates from Intensive Care Unit Patients and the Utility of Whole-Genome Sequencing in Health Care Settings

    Science.gov (United States)

    Hazen, Tracy H.; Zhao, LiCheng; Boutin, Mallory A.; Stancil, Angela; Robinson, Gwen; Harris, Anthony D.; Rasko, David A.

    2014-01-01

    The IncA/C plasmids have been implicated for their role in the dissemination of β-lactamases, including gene variants that confer resistance to expanded-spectrum cephalosporins, which are often the treatment of last resort against multidrug-resistant, hospital-associated pathogens. A blaFOX-5 gene was detected in 14 Escherichia coli and 16 Klebsiella isolates that were cultured from perianal swabs of patients admitted to an intensive care unit (ICU) of the University of Maryland Medical Center (UMMC) in Baltimore, MD, over a span of 3 years. Four of the FOX-encoding isolates were obtained from subsequent samples of patients that were initially negative for an AmpC β-lactamase upon admission to the ICU, suggesting that the AmpC β-lactamase-encoding plasmid was acquired while the patient was in the ICU. The genomes of five E. coli isolates and six Klebsiella isolates containing blaFOX-5 were selected for sequencing based on their plasmid profiles. An ∼167-kb IncA/C plasmid encoding the FOX-5 β-lactamase, a CARB-2 β-lactamase, additional antimicrobial resistance genes, and heavy metal resistance genes was identified. Another FOX-5-encoding IncA/C plasmid that was nearly identical except for a variable region associated with the resistance genes was also identified. To our knowledge, these plasmids represent the first FOX-5-encoding plasmids sequenced. We used comparative genomics to describe the genetic diversity of a plasmid encoding a FOX-5 β-lactamase relative to the whole-genome diversity of 11 E. coli and Klebsiella isolates that carry this plasmid. Our findings demonstrate the utility of whole-genome sequencing for tracking of plasmid and antibiotic resistance gene distribution in health care settings. PMID:24914121

  12. Comparative genomic analysis of two novel sporadic Shiga toxin-producing Escherichia coli O104:H4 strains isolated 2011 in Germany.

    Directory of Open Access Journals (Sweden)

    Erhard Tietze

    Full Text Available A large outbreak of gastrointestinal disease occurred in 2011 in Germany which resulted in almost 4000 patients with acute gastroenteritis or hemorrhagic colitis, 855 cases of a hemolytic uremic syndrome and 53 deaths. The pathogen was an uncommon, multiresistant Escherichia coli strain of serotype O104:H4 which expressed a Shiga toxin characteristic of enterohemorrhagic E. coli and in addition virulence factors common to enteroaggregative E. coli. During post-epidemic surveillance of Shiga toxin-producing E. coli (STEC all but two of O104:H4 isolates were indistinguishable from the epidemic strain. Here we describe two novel STEC O104:H4 strains isolated in close spatiotemporal proximity to the outbreak which show a virulence gene panel, a Shiga toxin-mediated cytotoxicity towards Vero cells and aggregative adherence to Hep-2 cells comparable to the outbreak strain. They differ however both from the epidemic strain and from each other, by their antibiotic resistance phenotypes and some other features as determined by routine epidemiological subtyping methods. Whole genome sequencing of these two strains, of ten outbreak strain isolates originating from different time points of the outbreak and of one historical sporadic EHEC O104:H4 isolate was performed. Sequence analysis revealed a clear phylogenetic distance between the two variant strains and the outbreak strain finally identifying them as epidemiologically unrelated isolates from sporadic cases. These findings add to the knowledge about this emerging pathogen, illustrating a certain diversity within the bacterial core genome as well as loss and gain of accessory elements. Our results do also support the view that distinct new variants of STEC O104:H4 repeatedly might originate from yet unknown reservoirs, rather than that there would be a continuous diversification of a single epidemic strain established and circulating in Germany after the large outbreak in 2011.

  13. Comparative genomic analysis of two novel sporadic Shiga toxin-producing Escherichia coli O104:H4 strains isolated 2011 in Germany.

    Science.gov (United States)

    Tietze, Erhard; Dabrowski, Piotr Wojciech; Prager, Rita; Radonic, Aleksandar; Fruth, Angelika; Auraß, Philipp; Nitsche, Andreas; Mielke, Martin; Flieger, Antje

    2015-01-01

    A large outbreak of gastrointestinal disease occurred in 2011 in Germany which resulted in almost 4000 patients with acute gastroenteritis or hemorrhagic colitis, 855 cases of a hemolytic uremic syndrome and 53 deaths. The pathogen was an uncommon, multiresistant Escherichia coli strain of serotype O104:H4 which expressed a Shiga toxin characteristic of enterohemorrhagic E. coli and in addition virulence factors common to enteroaggregative E. coli. During post-epidemic surveillance of Shiga toxin-producing E. coli (STEC) all but two of O104:H4 isolates were indistinguishable from the epidemic strain. Here we describe two novel STEC O104:H4 strains isolated in close spatiotemporal proximity to the outbreak which show a virulence gene panel, a Shiga toxin-mediated cytotoxicity towards Vero cells and aggregative adherence to Hep-2 cells comparable to the outbreak strain. They differ however both from the epidemic strain and from each other, by their antibiotic resistance phenotypes and some other features as determined by routine epidemiological subtyping methods. Whole genome sequencing of these two strains, of ten outbreak strain isolates originating from different time points of the outbreak and of one historical sporadic EHEC O104:H4 isolate was performed. Sequence analysis revealed a clear phylogenetic distance between the two variant strains and the outbreak strain finally identifying them as epidemiologically unrelated isolates from sporadic cases. These findings add to the knowledge about this emerging pathogen, illustrating a certain diversity within the bacterial core genome as well as loss and gain of accessory elements. Our results do also support the view that distinct new variants of STEC O104:H4 repeatedly might originate from yet unknown reservoirs, rather than that there would be a continuous diversification of a single epidemic strain established and circulating in Germany after the large outbreak in 2011.

  14. A Tale of Two Countries: Successes and Challenges in K-12 Computer Science Education in Israel and the United States

    Science.gov (United States)

    Gal-Ezer, Judith; Stephenson, Chris

    2014-01-01

    This article tells a story of K-12 computer science in two different countries. These two countries differ profoundly in culture, language, government and state structure, and in their education systems. Despite these differences, however, they share the pursuit of excellence and high standards in K-12 education. In Israel, curriculum is…

  15. One-to-One Technology in K-12 Classrooms: A Review of the Literature from 2004 through 2014

    Science.gov (United States)

    Harper, Ben; Milman, Natalie B.

    2016-01-01

    This literature review examined empirical research conducted between 2004 and 2014 regarding 1:1 technologies in K-12 educational settings. Our overarching research question was: What does research tell us about 1:1 technology in K-12 classrooms? We used the constant-comparative method to analyze, code, and induce themes from 46 relevant articles.…

  16. K-12 Students' Perceptions of Scientists: Finding a Valid Measurement and Exploring Whether Exposure to Scientists Makes an Impact

    Science.gov (United States)

    Hillman, Susan J.; Bloodsworth, Kylie H.; Tilburg, Charles E.; Zeeman, Stephan I.; List, Henrietta E.

    2014-01-01

    This study was launched from a National Science Foundation GK-12 grant in which graduate fellows in Science, Technology, Engineering, and Mathematics (STEM) are placed in classrooms to engage K-12 students in STEM activities. The investigation explored whether the STEM Fellows' presence impacted the K-12 students' stereotypical image of a…

  17. Synergistic effects in mixed Escherichia coli biofilms

    DEFF Research Database (Denmark)

    Reisner, A.; Holler, B.M.; Molin, Søren

    2006-01-01

    the pathways governing development of more complex heterogeneous communities. In this study, we established a laboratory model where biofilm-stimulating effects due to interactions between genetically diverse strains of Escherichia coli were monitored. Synergistic induction of biofilm formation resulting from...... the cocultivation of 403 undomesticated E. coli strains with a characterized E. coli K-12 strain was detected at a significant frequency. The survey suggests that different mechanisms underlie the observed stimulation, yet synergistic development of biofilm within the subset of E. coli isolates (n = 56) exhibiting...... the strongest effects was most often linked to conjugative transmission of natural plasmids carried by the E. coli isolates (70%). Thus, the capacity of an isolate to promote the biofilm through cocultivation was (i) transferable to the K-12 strain, (ii) was linked with the acquisition of conjugation genes...

  18. Discovery of Escherichia coli CRISPR sequences in an undergraduate laboratory.

    Science.gov (United States)

    Militello, Kevin T; Lazatin, Justine C

    2017-05-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) represent a novel type of adaptive immune system found in eubacteria and archaebacteria. CRISPRs have recently generated a lot of attention due to their unique ability to catalog foreign nucleic acids, their ability to destroy foreign nucleic acids in a mechanism that shares some similarity to RNA interference, and the ability to utilize reconstituted CRISPR systems for genome editing in numerous organisms. In order to introduce CRISPR biology into an undergraduate upper-level laboratory, a five-week set of exercises was designed to allow students to examine the CRISPR status of uncharacterized Escherichia coli strains and to allow the discovery of new repeats and spacers. Students started the project by isolating genomic DNA from E. coli and amplifying the iap CRISPR locus using the polymerase chain reaction (PCR). The PCR products were analyzed by Sanger DNA sequencing, and the sequences were examined for the presence of CRISPR repeat sequences. The regions between the repeats, the spacers, were extracted and analyzed with BLASTN searches. Overall, CRISPR loci were sequenced from several previously uncharacterized E. coli strains and one E. coli K-12 strain. Sanger DNA sequencing resulted in the discovery of 36 spacer sequences and their corresponding surrounding repeat sequences. Five of the spacers were homologous to foreign (non-E. coli) DNA. Assessment of the laboratory indicates that improvements were made in the ability of students to answer questions relating to the structure and function of CRISPRs. Future directions of the laboratory are presented and discussed. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):262-269, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

  19. K-12 Neuroscience Education Outreach Program: Interactive Activities for Educating Students about Neuroscience

    Science.gov (United States)

    Deal, Alex L.; Erickson, Kristen J.; Bilsky, Edward J.; Hillman, Susan J.; Burman, Michael A.

    2014-01-01

    The University of New England’s Center for Excellence in the Neurosciences has developed a successful and growing K-12 outreach program that incorporates undergraduate and graduate/professional students. The program has several goals, including raising awareness about fundamental issues in neuroscience, supplementing science education in area schools and enhancing undergraduate and graduate/professional students’ academic knowledge and skill set. The outreach curriculum is centered on core neuroscience themes including: Brain Safety, Neuroanatomy, Drugs of Abuse and Addiction, Neurological and Psychiatric Disorders, and Cognition and Brain Function. For each theme, lesson plans were developed based upon interactive, small-group activities. Additionally, we’ve organized our themes in a “Grow-up, Grow-out” approach. Grow-up refers to returning to a common theme, increasing in complexity as we revisit students from early elementary through high school. Grow-out refers to integrating other scientific fields into our lessons, such as the chemistry of addiction, the physics of brain injury and neuronal imaging. One of the more successful components of our program is our innovative team-based model of curriculum design. By creating a team of undergraduate, graduate/professional students and faculty, we create a unique multi-level mentoring opportunity that appears to be successful in enhancing undergraduate students’ skills and knowledge. Preliminary assessments suggest that undergraduates believe they are enhancing their content knowledge and professional skills through our program. Additionally, we’re having a significant, short-term impact on K-12 interest in science. Overall, our program appears to be enhancing the academic experience of our undergraduates and exciting K-12 students about the brain and science in general. PMID:25565921

  20. K-12 Neuroscience Education Outreach Program: Interactive Activities for Educating Students about Neuroscience.

    Science.gov (United States)

    Deal, Alex L; Erickson, Kristen J; Bilsky, Edward J; Hillman, Susan J; Burman, Michael A

    2014-01-01

    The University of New England's Center for Excellence in the Neurosciences has developed a successful and growing K-12 outreach program that incorporates undergraduate and graduate/professional students. The program has several goals, including raising awareness about fundamental issues in neuroscience, supplementing science education in area schools and enhancing undergraduate and graduate/professional students' academic knowledge and skill set. The outreach curriculum is centered on core neuroscience themes including: Brain Safety, Neuroanatomy, Drugs of Abuse and Addiction, Neurological and Psychiatric Disorders, and Cognition and Brain Function. For each theme, lesson plans were developed based upon interactive, small-group activities. Additionally, we've organized our themes in a "Grow-up, Grow-out" approach. Grow-up refers to returning to a common theme, increasing in complexity as we revisit students from early elementary through high school. Grow-out refers to integrating other scientific fields into our lessons, such as the chemistry of addiction, the physics of brain injury and neuronal imaging. One of the more successful components of our program is our innovative team-based model of curriculum design. By creating a team of undergraduate, graduate/professional students and faculty, we create a unique multi-level mentoring opportunity that appears to be successful in enhancing undergraduate students' skills and knowledge. Preliminary assessments suggest that undergraduates believe they are enhancing their content knowledge and professional skills through our program. Additionally, we're having a significant, short-term impact on K-12 interest in science. Overall, our program appears to be enhancing the academic experience of our undergraduates and exciting K-12 students about the brain and science in general.

  1. Participative Teaching with Mobile Devices and Social Networks for K-12 Children

    Directory of Open Access Journals (Sweden)

    Livia Stefan

    2016-08-01

    Full Text Available This article details a set of participatory pedagogical experiments conducted within a research grant PN II IDEI (”Time Maps. Real communities, virtual worlds, experimented pasts” performed with the purpose of helping rural communities in identifying their cultural heritage andtransmitting it to the younger generations by means of modern IT technologies, including web 2.0. In a Danubian rural community, several points of archaeological interest (POIs were identified, which were then included in a geographic Augmented Reality application for smartphones and tablets. Subsequently, the geographic data were collected from the archaeological site by the K-12 children, under the coordination of an academic staff member of the National University of Arts in Bucharest, and stored on their devices using Google Maps. The augmented information provided onthe site was annotated and shared with other K-12 children, through different social networks sites (SNS and content postings. This first stage experiment was extended to the development of a social learning environment complementary to the educational site (www.timemaps.net to support thetransmission of several traditional technologies (textile, ceramic, glass in a collaborative manner. We consider that our experiments can significantly increase the visibility of the information pertaining to the identity of target places and communities among the younger generation. A mobile-learning paradigm, in combination with web 2.0 technologies, was the support for a distributed and low-cost platform for communication and collaboration. Social networks linked thearchaeological heritage and the academic research with the larger community of rural K-12 children. The article analyzes this platform as a solution for creating, collecting and sharingeducational content, and presents conclusions on using social media for effective blended learning and transmittal of the cultural heritage.

  2. Sense and Sensibility: The Case for the Nationwide Inclusion of Engineering in the K-12 Curriculum

    Science.gov (United States)

    Lindberg, Robert E.; Pinelli, Thomas E.; Batterson, James G.

    2008-01-01

    The competitive status of the United States is inextricably linked to innovation just as innovation is inseparable from science, technology, engineering, and mathematics. To stay competitive in innovation requires that the United States produce a 21st century workforce complete with requisite education, training, skills, and motivation. If we accept a priori that science, technology, engineering, and mathematics education are crucial to competitiveness and innovation and that, in terms of innovation, mathematics, science, and engineering are interdependent, why are mathematics and science uniformly ubiquitous in the K-12 curriculum while engineering is conspicuously absent? We are passionate in our belief that the uniform addition of engineering to the K-12 curriculum will help ensure that the nation has "the right" 21st Century workforce. Furthermore, we believe that a nationwide effort, led by a coalition of engineering academics, practitioners, and societies is required to turn this goal into reality. However, accomplishing this goal necessitates, as we are reminded by the title of Jane Austen's timeless novel, "Sense and Sensibility", a workable solution that seeks the "middle ground" between passion and reason. We begin our paper by making two essential points: Engineers are not scientists. Engineering exists separate from science, has its own specialized knowledge community apart from science, and it is largely responsible for many of the most significant advancements and improvements in the quality of our life. Our workable solution requires that K-12 education, nationwide, accommodate the inclusion of engineering as a stand alone curriculum and we offer three reasons to support our position: (1) workforce development, (2) stimulating interest in STEM (science, technology, engineering, and mathematics) courses and careers, and (3) creating a technologically literate society. We conclude with some thoughts on how this important goal can be accomplished.

  3. Making NASA Earth Observing System Satellite Data Accessible to the K-12 and Citizen Scientist Communities

    Science.gov (United States)

    Moore, Susan W.; Phelps, Carrie S.; Chambers, Lin H.

    2004-01-01

    The Atmospheric Sciences Data Center (ASDC) at NASA s Langley Research Center houses over 700 data sets related to Earth s radiation budget, clouds, aerosols and tropospheric chemistry. These data sets are produced to increase academic understanding of the natural and anthropogenic perturbations that influence global climate change. The Mentoring and inquirY using NASA Data on Atmospheric and earth science for Teachers and Amateurs (MY NASA DATA) project has been established to systematically support educational activities at all levels of formal and informal education by reducing these large data holdings to microsets that will be easily explored and understood by the K-12 and the amateur scientist communities

  4. Use of Streptococcus salivarius K12 in the prevention of streptococcal and viral pharyngotonsillitis in children.

    Science.gov (United States)

    Di Pierro, Francesco; Colombo, Maria; Zanvit, Alberto; Risso, Paolo; Rottoli, Amilcare S

    2014-01-01

    Streptococcus salivarius K12 is an oral probiotic strain releasing two lantibiotics (salivaricin A2 and salivaricin B) that antagonize the growth of S. pyogenes, the most important bacterial cause of pharyngeal infections in humans also affected by episodes of acute otitis media. S. salivarius K12 successfully colonizes the oral cavity, and is endowed with an excellent safety profile. We tested its preventive role in reducing the incidence of both streptococcal and viral pharyngitis and/or tonsillitis in children. We enrolled 61 children with a diagnosis of recurrent oral streptococcal disorders. Thirty-one of them were enrolled to be treated daily for 90 days with a slow-release tablet for oral use, containing no less than 1 billion colony-forming units/tablet of S. salivarius K12 (Bactoblis®), and the remaining 30 served as the untreated control group. During treatment, they were all examined for streptococcal infection. Twenty children (ten per group) were also assessed in terms of viral infection. Secondary end points in both groups were the number of days under antibiotic and antipyretic therapy and the number of days off school (children) and off work (parents). The 30 children who completed the 90-day trial with Bactoblis® showed a significant reduction in their episodes of streptococcal pharyngeal infection (>90%), as calculated by comparing the infection rates of the previous year. No difference was observed in the control group. The treated group showed a significant decrease in the incidence (80%) of oral viral infections. Again, there was no difference in the control group. With regard to secondary end points, the number of days under antibiotic treatment of the treated and control groups were 30 and 900 respectively, days under antipyretic treatment 16 and 228, days of absence from school 16 and 228, and days of absence from work 16 and 228. The product was well tolerated by the subjects, with no side effects, and only one individual reported bad

  5. The Next Generation Science Standards: An Historic Opportunity for K-12 Earth and Space Science Education

    Science.gov (United States)

    Johnson, R. M.; Passow, M. J.; Holzer, M. A.; Moore, J.

    2014-12-01

    The Next Generation Science Standards (NGSS) provide an historic opportunity to significantly improve Earth and space science (ESS) education nationally at the K-12 level. The increased emphasis on ESS related topics in the NGSS relative to previous standards provides a real opportunity for ensuring all K-12 students in adopting states learn about the ESS - allowing us to reach many more students than are currently are exposed to our discipline. The new standards are also exciting in that they explicitly couple science and engineering practice, cross-cutting concepts, and disciplinary core ideas in such a way that student must actively demonstrate their understanding through actions rather than through mere regurgitation of memorized responses. Achieving mastery of NGSS Performance Expectations will require practice with higher-order learning skills - with students engaging in the practices of scientists and engineers. Preparing students for this mastery will be a challenging task for teachers, since in many states professional development support is limited at best for the current curriculum - let alone the curricula that will be developed to address the NGSS. As adoption of the NGSS expands across the country, states will be at various levels of implementation of the new standards over the next several years - and there is real concern that teachers must have sufficient professional development to be able to be successful in preparing their students - particularly in view of likely coupled assessments and teacher evaluations. NESTA strongly supports implementation of the NGSS, and the rigorous and compelling ESS education it will engender, when coupled with a strong emphasis nationwide on teacher professional development. For the past two years, the National Earth Science Teachers Association (NESTA) has continued our leadership in K-12 ESS education through workshops, web seminars, events and publications that emphasize implementation of the NGSS in ESS

  6. Sustaining K-12 professional development in geology: Recurrent participation in Rockcamp

    Science.gov (United States)

    Repine, T.E.; Hemler, D.A.; Behling, R.E.

    2004-01-01

    A reconnaissance study of the geology professional development program known as RockCamp was initiated to examine the sustained, or recurrent, participation of K-12 science teachers. Open-ended interviews, concept mapping, and creative writing assignments were used to explore the perceptions of six teachers possessing an exceptional record of participation. Efficacy, fun, right time of life, and support emerged as unanimous reasons for recurrent participation. Content, friendship, and methodology were very important. College credit was not critical. These teachers' perceptions suggest their sustained involvement in the RockCamp Program is stimulated by situated learning experiences stressing a compare, contrast, connect, and construct pedagogy within a supportive learning community.

  7. Educating K-12 Professionals and Parents: Finding Health Information for Special Needs Children.

    Science.gov (United States)

    Irish, D Elizabeth; Lyman, Deborah M; Squillace, Helen A; Geyer, Enid M; Cosgrove, Tammy D; Hagzan, Amanda; Leinung, Jill; Tosh, Traci

    2015-01-01

    A successful partnership model between an academic health sciences library and a K-12 school district to provide librarians, nurses, and special education staff with access to health information to support special needs children and their parents is presented. Train-the-trainer staff sessions and a parent session were collaboratively developed. Funding support was used to purchase iPads for librarians and nurses to deliver mobile support. The results indicate the resources taught are being used to find health information and the school librarians and nurses are being sought after to assist in finding health information. Positive feedback from the school district indicates this model could be replicated in similar settings.

  8. Accurate Dna Assembly And Direct Genome Integration With Optimized Uracil Excision Cloning To Facilitate Engineering Of Escherichia Coli As A Cell Factory

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Kim, Se Hyeuk; Nørholm, Morten

    2015-01-01

    Plants produce a vast diversity of valuable compounds with medical properties, but these are often difficult to purify from the natural source or produce by organic synthesis. An alternative is to transfer the biosynthetic pathways to an efficient production host like the bacterium Escherichia co......-excision-based cloning and combining it with a genome-engineering approach to allow direct integration of whole metabolic pathways into the genome of E. coli, to facilitate the advanced engineering of cell factories........ Cloning and heterologous gene expression are major bottlenecks in the metabolic engineering field. We are working on standardizing DNA vector design processes to promote automation and collaborations in early phase metabolic engineering projects. Here, we focus on optimizing the already established uracil...

  9. Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii.

    Science.gov (United States)

    Lindsey, Rebecca L; Garcia-Toledo, L; Fasulo, D; Gladney, L M; Strockbine, N

    2017-09-01

    Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E. coli, 5 Shigella spp., 21 E. albertii, 12 E. fergusonii and 5 other species) and design primers for the following species-specific regions: a 212bp region of the cyclic di-GMP regulator gene (cdgR, AW869_22935 from genome K-12 MG1655, CP014225) for E. coli/Shigella; a 393bp region of the DNA-binding transcriptional activator of cysteine biosynthesis gene (EAKF1_ch4033 from genome KF1, CP007025) for E. albertii; and a 575bp region of the palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase (EFER_0790 from genome ATCC 35469, CU928158) for E. fergusonii. We incorporated the species-specific primers into a conventional multiplex PCR assay and assessed its performance with a collection of 97 Enterobacteriaceae strains. The assay was 100% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies. Published by Elsevier B.V.

  10. Oligo- and dsDNA-mediated genome editing using a tetA dual selection system in Escherichia coli

    National Research Council Canada - National Science Library

    Young Shin Ryu; Sathesh-Prabu Chandran; Kyungchul Kim; Sung Kuk Lee

    2017-01-01

    .... Herein, we report on a promising method in Escherichia coli that relies on the insertion of an optimized tetA dual selection cassette followed by replacement of the same cassette with short, single-stranded DNA (oligos...

  11. Restructuring the relationship between STEM faculty and K-12: crafting a figured world of partnership

    Science.gov (United States)

    Fayez, Merfat

    2010-09-01

    Over the past 50 years, identity has provided us with a dynamic tool to understand and examine how people are constituted as agents as well as subjects of culturally constructed, socially enacted worlds. Pertinent to this conceptualization, Skerrett and Sevian focus on science and mathematics faculty's identities and seek to understand how certain aspects of their identities mediate certain motivations to involvement in K-12 service. While I believe that the authors presented an affluent discussion of agency from the perspective of identity, I think that if we are to understand agency from a sociocultural perspective, we have to magnify a view of identity and agency in the figured world of practice/activity. My main goal is not only to reclaim the importance of the individual dimension and agency within a profoundly social view of the self, but also to highlight the figured contextual factors that would either enable or constrain STEM faculty's involvement in K-12 outreach. After first outlining the perspective of identity and agency that was adopted by Skerrett and Sevian, I extend the discussion of Skerrett and Sevian to move forward toward a figured world of partnership. I conclude by positing that the third generation of activity theory has a potential for contributing to our understanding of how the social institutional context and its structure is important to our understanding of individual agency.

  12. A Meta-Analysis of Self-Monitoring on Reading Performance of K-12 Students.

    Science.gov (United States)

    Guzman, Guadalupe; Goldberg, Taryn S; Swanson, H Lee

    2017-03-16

    The published single-case design (SCD) research (N = 19 articles) on self-monitoring and reading performance was synthesized. The following inclusion criteria were used: (a) the study must have been peer-reviewed, (b) implemented an intervention targeting student self-monitoring of reading skills, (c) included data on at least 1 reading outcome, (d) included visual representation of the data, and (f) the study must have used an SCD to assess the topic of interest. A total of 67 participants, 45 males and 22 females, ranging in age from 7:8 -18:7 were included in the current meta-analysis. Ethnicity was reported for 42 students: 23 were Caucasian, 12 were African American, and 7 were Latino/Hispanic. Studies were compared with those meeting What Works Clearinghouse (WWC) standards and those not meeting standards. The Tau-U effect size (ES) method was the main calculation method used; however, Phi ES estimates are included for comparison purposes. Results indicated that self-monitoring had an overall significant large positive effect on the reading performance of K-12 students, Tau-U = 0.79, 95% confidence interval (CI) [0.64, 0.93], p reading intervention for students in Grades K-12. Furthermore, findings indicate that larger ES values were identified when consolidating studies based on WWC guidelines as compared with consolidating across all studies. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  13. Pay It Forward: Teacher Candidates’ Use of Historical Artifacts to Invigorate K-12 History Instruction

    Directory of Open Access Journals (Sweden)

    Scott M. Waring,

    2015-11-01

    Full Text Available The history education literature is replete with a call to help teachers understand that history should be taught as being inquiry-based and interpretive. We are encouraged, and rightfully so, to do history, to perform history, to do democracy, and to motivate students for inquiry and action by using primary sources. The authors developed a unit of study for history and social studies teacher candidates that would address several issues: (a motivate and inspire future teachers to use inquiry as a tool to build K-12 students’ historical understanding and facilitate purposeful utilization of artifacts with ease; (b help future teachers increase their knowledge of local history; and (c present a unit that could be easily used in a secondary history course and, with some modifications, could be adapted for elementary and middle school history classrooms. The assignment was named Pay it Forward: Invigorating Instruction through Local History. This multifaceted assignment included the development of a lesson plan that would (a demonstrate a robust understanding of engaging students in historical inquiry and local history, and (b focus on an artifact that the teacher candidate would find as part of the investigation. The majority of the teacher candidates in this study did show evidence of, albeit limited at times, designing curriculum that encouraged K-12 students to engage in historical inquiry. Making the bridge between theory and practice, or showing evidence of learning from the methods courses, was clearly evident across the lesson plans.

  14. Implications of the Next Generation Science Standards for K-12, EPO, and Higher Education

    Science.gov (United States)

    Schultz, G.; Barber, J.; Pomeroy, R.; Reagan, G.

    2014-07-01

    The newly-released Next Generation Science Standards (NGSS) have been under development for a few years with broad community input and explicit involvement of many states likely to adopt these as their own science standards. Several key features of the NGSS make these a substantial advance from the existing National Science Education Standards (NRC 1996), including focus on three dimensions previously outlined in A Framework for K-12 Science Education (NRC 2011): Science and Engineering Practices; Cross-cutting Concepts; and Disciplinary Core Ideas. What are the implications of all this now for K-12 educators, in the immediate term and in the long-term? What do the NGSS imply for EPO professionals, especially those involved in science curriculum development and teacher professional development? What should higher education faculty know about the NGSS, especially as it relates to the preparation of incoming college students, as well as the education of future elementary and secondary science teachers in college (including in Astro 101-type courses)?

  15. simUfish: An Interactive Application to Teach K-12 Students About Zebrafish Behavior.

    Science.gov (United States)

    Mwaffo, Violet; Korneyeva, Veronika; Porfiri, Maurizio

    2017-10-01

    As the zebrafish is rapidly becoming a species of choice in preclinical research, several efforts are being placed toward creating educational programs for K-12 students based on this promising model organism. However, as any other model organisms, the use of zebrafish in classroom settings requires additional experimental resources and poses ethical challenges related to animal use. To mitigate these factors, we have developed an application (app), simUfish, which implements a mathematical model of zebrafish behavior for generating multiple fish trajectories and animating their body undulations. simUfish is developed using a multiplatform game engine and is expected to promote the knowledge of zebrafish behavior to both K-12 students and the general public. Specifically, it demonstrates basic principles of fish individual and social behaviors, including environment interaction; fear response toward a predator; shoaling; and attraction toward a stimulus, which can be a food source or simply a finger placed on the touch screen. The effectiveness of the app as an accessible experimental tool for learning was tested in an outreach activity on middle school students from the New York City school system. The results from this activity show an immediate, tangible improvement of students' satisfaction and willingness to learn about key concepts on zebrafish behavior, accompanied by high level of interest in life sciences.

  16. The Analysis of Multiple Genome Comparisons in Genus Escherichia and Its Application to the Discovery of Uncharacterised Metabolic Genes in Uropathogenic Escherichia coli CFT073

    Directory of Open Access Journals (Sweden)

    William A. Bryant

    2009-01-01

    Full Text Available A survey of a complete gene synteny comparison has been carried out between twenty fully sequenced strains from the genus Escherichia with the aim of finding yet uncharacterised genes implicated in the metabolism of uropathogenic strains of E. coli (UPEC. Several sets of adjacent colinear genes have been identified which are present in all four UPEC included in this study (CFT073, F11, UTI89, and 536, annotated with putative metabolic functions, but are not found in any other strains considered. An operon closely homologous to that encoding the L-sorbose degradation pathway in Klebsiella pneumoniae has been identified in E. coli CFT073; this operon is present in all of the UPEC considered, but only in 7 of the other 16 strains. The operon's function has been confirmed by cloning the genes into E. coli DH5α and testing for growth on L-sorbose. The functional genomic approach combining in silico and in vitro work presented here can be used as a basis for the discovery of other uncharacterised genes contributing to bacterial survival in specific environments.

  17. Genomic, proteomic and physiological characterization of a T5-like bacteriophage for control of Shiga toxin-producing Escherichia coli O157:H7.

    Science.gov (United States)

    Niu, Yan D; Stanford, Kim; Kropinski, Andrew M; Ackermann, Hans-Wolfgang; Johnson, Roger P; She, Yi-Min; Ahmed, Rafiq; Villegas, Andre; McAllister, Tim A

    2012-01-01

    Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33), a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli. Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31 × 10(-9) ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C), containing 160 open reading frames (ORFs), 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (National Centre for Biotechnology Information database. AKVF33 also lacked the L-shaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37-41%) to tail fibers of E. coli phage phiEco32 of Podoviridae, a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein (pb5) shared an overall identify of 29-72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip (pb2). The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre- and post-harvest biocontrol agent.

  18. Genomic, proteomic and physiological characterization of a T5-like bacteriophage for control of Shiga toxin-producing Escherichia coli O157:H7.

    Directory of Open Access Journals (Sweden)

    Yan D Niu

    Full Text Available Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7 continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33, a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli. Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31 × 10(-9 ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C, containing 160 open reading frames (ORFs, 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (<60% to proteins in the National Centre for Biotechnology Information database. AKVF33 also lacked the L-shaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37-41% to tail fibers of E. coli phage phiEco32 of Podoviridae, a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein (pb5 shared an overall identify of 29-72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip (pb2. The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre- and post-harvest biocontrol agent.

  19. The genome and proteome of a virulent Escherichia coli O157:H7 bacteriophage closely resembling Salmonella phage Felix O1

    Directory of Open Access Journals (Sweden)

    Waddell Thomas E

    2009-04-01

    Full Text Available Abstract Based upon whole genome and proteome analysis, Escherichia coli O157:H7-specific bacteriophage (phage wV8 belongs to the new myoviral genus, "the Felix O1-like viruses" along with Salmonella phage Felix O1 and Erwinia amylovora phage φEa21-4. The genome characteristics of phage wV8 (size 88.49 kb, mol%G+C 38.9, 138 ORFs, 23 tRNAs are very similar to those of phage Felix O1 (86.16 kb, 39.0 mol%G+C, 131 ORFs and 22 tRNAs and, indeed most of the proteins have their closest homologs within Felix O1. Approximately one-half of the Escherichia coli O157:H7 mutants resistant to phage wV8 still serotype as O157:H7 indicating that this phage may recognize, like coliphage T4, two different surface receptors: lipopolysaccharide and, perhaps, an outer membrane protein.

  20. Evidence of horizontal gene transfer between human and animal commensal Escherichia coli strains identified by microarray.

    Science.gov (United States)

    Grasselli, Elena; François, Patrice; Gutacker, Michaela; Gettler, Brian; Benagli, Cinzia; Convert, Maruska; Boerlin, Patrick; Schrenzel, Jacques; Piffaretti, Jean-Claude

    2008-08-01

    Bacteria exchange genetic material by horizontal gene transfer (HGT). To evaluate the impact of HGT on Escherichia coli genome plasticity, 19 commensal strains collected from the intestinal floras of humans and animals were analyzed by microarrays. Strains were hybridized against an oligoarray containing 2700 E. coli K12 chromosomal genes. A core (genes shared among compared genomes) and a flexible gene pool (genes unique for each genome) have been identified. Analysis of hybridization signals evidenced 1015 divergent genes among the 19 strains and each strain showed a specific genomic variability pattern. Four hundred and fifty-eight genes were characterized by higher rates of interstrain variation and were considered hyperdivergent. These genes are not randomly distributed onto the chromosome but are clustered in precise regions. Hyperdivergent genes belong to the flexible gene pool and show a specific GC content, differing from that of the chromosome, indicating acquisition by HGT. Among these genes, those involved in defense mechanisms and cell motility as well as intracellular trafficking and secretion were far more represented than others. The observed genome plasticity contributes to the maintenance of genetic diversity and may therefore be a source of evolutionary adaptation and survival.