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Sample records for high-copy t7 escherichia

  1. Simultaneous Binding of Multiple EF-Tu Copies to Translating Ribosomes in Live Escherichia coli.

    Science.gov (United States)

    Mustafi, Mainak; Weisshaar, James C

    2018-01-16

    In bacteria, elongation factor Tu is a translational cofactor that forms ternary complexes with aminoacyl-tRNA (aa-tRNA) and GTP. Binding of a ternary complex to one of four flexible L7/L12 units on the ribosome tethers a charged tRNA in close proximity to the ribosomal A site. Two sequential tests for a match between the aa-tRNA anticodon and the current mRNA codon then follow. Because one elongation cycle can occur in as little as 50 ms and the vast majority of aa-tRNA copies are not cognate with the current mRNA codon, this testing must occur rapidly. We present a single-molecule localization and tracking study of fluorescently labeled EF-Tu in live Escherichia coli Imaging at 2 ms/frame distinguishes 60% slowly diffusing EF-Tu copies (assigned as transiently bound to translating ribosome) from 40% rapidly diffusing copies (assigned as a mixture of free ternary complexes and free EF-Tu). Combining these percentages with copy number estimates, we infer that the four L7/L12 sites are essentially saturated with ternary complexes in vivo. The results corroborate an earlier inference that all four sites can simultaneously tether ternary complexes near the A site, creating a high local concentration that may greatly enhance the rate of testing of aa-tRNAs. Our data and a combinatorial argument both suggest that the initial recognition test for a codon-anticodon match occurs in less than 1 to 2 ms per aa-tRNA copy. The results refute a recent study (A. Plochowietz, I. Farrell, Z. Smilansky, B. S. Cooperman, and A. N. Kapanidis, Nucleic Acids Res 45:926-937, 2016, https://doi.org/10.1093/nar/gkw787) of tRNA diffusion in E. coli that inferred that aa-tRNAs arrive at the ribosomal A site as bare monomers, not as ternary complexes. IMPORTANCE Ribosomes catalyze translation of the mRNA codon sequence into the corresponding sequence of amino acids within the nascent polypeptide chain. Polypeptide elongation can be as fast as 50 ms per added amino acid. Each amino acid

  2. Crystallization and preliminary crystallographic analysis of tRNA (m7G46) methyltransferase from Escherichia coli

    International Nuclear Information System (INIS)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun; Niu, Liwen

    2008-01-01

    tRNA (m 7 G46) methyltransferase from E. coli was overexpressed, purified and crystallized. Diffraction data were collected to 2.04 Å resolution. Transfer RNA (tRNA) (m 7 G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-l-methionine (SAM) as the methyl-group donor to catalyze the formation of N 7 -methylguanosine (m 7 G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His 6 tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P2 1

  3. Genomic Variability of O Islands Encoding Tellurite Resistance in Enterohemorrhagic Escherichia coli O157:H7 Isolates

    Science.gov (United States)

    Taylor, Diane E.; Rooker, Michelle; Keelan, Monika; Ng, Lai-King; Martin, Irene; Perna, Nicole T.; Burland, N. T. Valerie; Blattner, Fredrick R.

    2002-01-01

    Strains of Escherichia coli causing enterohemorrhagic colitis belonging to the O157:H7 lineage are reported to be highly related. Fifteen strains of E. coli O157:H7 and 1 strain of E. coli O46:H− (nonflagellated) were examined for the presence of potassium tellurite resistance (Ter). Ter genes comprising terABCDEF were shown previously to be part of a pathogenicity island also containing integrase, phage, and urease genes. PCR analysis, both conventional and light cycler based, demonstrated that about one-half of the Ter E. coli O157:H7 strains (6 of 15), including the Sakai strain, which has been sequenced, carried a single copy of the Ter genes. Five of the strains, including EDL933, which has also been sequenced, contained two copies. Three other O157:H7 strains and the O46:H− strain did not contain the Ter genes. In strains containing two copies, the Ter genes were associated with the serW and serX tRNA genes. Five O157:H7 strains resembled the O157 Sakai strain whose sequence contained one copy, close to serX, whereas in one isolate the single copy was associated with serW. There was no correlation between Ter and the ability to produce Shiga toxin ST1 or ST2. The Ter MIC for most strains, containing either one or two copies, was 1,024 μg/ml, although for a few the MIC was intermediate, 64 to 128 μg/ml, which could be increased to 512 μg/ml by pregrowth of strains in subinhibitory concentrations of potassium tellurite. Reverse transcriptase PCR analysis confirmed that in most strains Ter was constitutive but that in the rest it was inducible and involved induction of terB and terC genes. Only the terB, -C, -D, and -E genes are required for Ter. The considerable degree of homology between the ter genes on IncH12 plasmid R478, which originated in Serratia marcescens, and pTE53, from an E. coli clinical isolate, suggests that the pathogenicity island was acquired from a plasmid. This work demonstrates diversity among E. coli O157:H7 isolates, at least as

  4. Crystallization and preliminary crystallographic analysis of tRNA (m{sup 7}G46) methyltransferase from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun, E-mail: mkteng@ustc.edu.cn; Niu, Liwen, E-mail: mkteng@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027 (China)

    2008-08-01

    tRNA (m{sup 7}G46) methyltransferase from E. coli was overexpressed, purified and crystallized. Diffraction data were collected to 2.04 Å resolution. Transfer RNA (tRNA) (m{sup 7}G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-l-methionine (SAM) as the methyl-group donor to catalyze the formation of N{sup 7}-methylguanosine (m{sup 7}G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His{sub 6} tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P2{sub 1}.

  5. FabV/Triclosan Is an Antibiotic-Free and Cost-Effective Selection System for Efficient Maintenance of High and Medium-Copy Number Plasmids in Escherichia coli.

    Science.gov (United States)

    Ali, Syed A; Chew, Yik Wei

    2015-01-01

    Antibiotic resistance genes and antibiotics are frequently used to maintain plasmid vectors in bacterial hosts such as Escherichia coli. Due to the risk of spread of antibiotic resistance, the regulatory authorities discourage the use of antibiotic resistance genes/antibiotics for the maintenance of plasmid vectors in certain biotechnology applications. Overexpression of E. coli endogenous fabI gene and subsequent selection on Triclosan has been proposed as a practical alternative to traditional antibiotic selection systems. Unfortunately, overexpression of fabI cannot be used to select medium-copy number plasmids, typically used for the expression of heterologous proteins in E. coli. Here we report that Vibrio cholera FabV, a functional homologue of E. coli FabI, can be used as a suitable marker for the selection and maintenance of both high and medium-copy number plasmid vectors in E. coli.

  6. The Escherichia coli argW-dsdCXA genetic island is highly variable, and E. coli K1 strains commonly possess two copies of dsdCXA.

    Science.gov (United States)

    Moritz, Rebecca L; Welch, Rodney A

    2006-11-01

    The genome sequences of Escherichia coli pathotypes reveal extensive genetic variability in the argW-dsdCXA island. Interestingly, the archetype E. coli K1 neonatal meningitis strain, strain RS218, has two copies of the dsdCXA genes for d-serine utilization at the argW and leuX islands. Because the human brain contains d-serine, an epidemiological study emphasizing K1 isolates surveyed the dsdCXA copy number and function. Forty of 41 (97.5%) independent E. coli K1 isolates could utilize d-serine. Southern blot hybridization revealed physical variability within the argW-dsdC region, even among 22 E. coli O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two dsdCXA loci. Mutational analysis indicated that each of the dsdA genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use d-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic E. coli (DEC) collection have this activity. The genome sequence of diarrheagenic E. coli isolates indicates that the csrRAKB genes for sucrose utilization are often substituted for dsdC and a portion of dsdX present at the argW-dsdCXA island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus d-serine utilization. The ability to use d-serine is a trait strongly selected for among E. coli K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic E. coli pathotypes appear to have substituted sucrose for d-serine as a potential nutrient.

  7. Valyl-tRNA synthetase gene of Escherichia coli K12: Molecular genetic characterization and homology within a family of aminoacyl-tRNA synthetases

    International Nuclear Information System (INIS)

    Heck, J.D. III.

    1988-01-01

    This work reports the subcloning and characterization of the molecular elements necessary for the expression of the Escherichia coli valS gene encoding valyl-tRNA synthetase. The valS gene was subcloned from plasmid pLC26-22 by genetic complementation of a valS ts strain. The DNA region encoding the valS structural gene was determined by in vitro coupled transcription-translation assays. Cells transformed with a plasmid containing a full length copy of the valS gene enhanced in vivo valyl-tRNA synthetase specific activity twelve-fold. DNA sequences flanking the valS structural gene are presented. The transcription initiation sites of the valS gene were determined, in vivo and in vitro, by S1 nuclease protection studies, primer-extension analysis and both [α- 32 P]labeled and [γ- 32 P]end-labeled in vitro transcription assays. The DNA sequence of the valS gene of Escherichia coli has been determined. Significant similarity at the primary sequence level was detected between valyl-tRNA synthetase of E. coli and other known branched-chain aminoacyl-tRNA synthetases. An extended open reading frame (ORF) encoded on the DNA strand opposite the valS structural gene is described

  8. 18 CFR 45.7 - Form of application; number of copies.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Form of application; number of copies. 45.7 Section 45.7 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... in accordance with § 131.60 of this chapter. Each copy shall bear the date and signature that appear...

  9. Genomic Variability of O Islands Encoding Tellurite Resistance in Enterohemorrhagic Escherichia coli O157:H7 Isolates

    OpenAIRE

    Taylor, Diane E.; Rooker, Michelle; Keelan, Monika; Ng, Lai-King; Martin, Irene; Perna, Nicole T.; Burland, N. T. Valerie; Blattner, Fredrick R.

    2002-01-01

    Strains of Escherichia coli causing enterohemorrhagic colitis belonging to the O157:H7 lineage are reported to be highly related. Fifteen strains of E. coli O157:H7 and 1 strain of E. coli O46:H− (nonflagellated) were examined for the presence of potassium tellurite resistance (Ter). Ter genes comprising terABCDEF were shown previously to be part of a pathogenicity island also containing integrase, phage, and urease genes. PCR analysis, both conventional and light cycler based, demonstrated t...

  10. m/sup 7/Guanosine in tRNA of Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Shugart, L; Chastain, B

    1979-01-01

    The nucleoside content of six different individual tRNAs was re-investigated. Particular emphasis was placed on obtaining an accurate, quantitative estimation of the amount of the minor nucleoside m/sup 7/guanosine which was found to occur at less than one full residue in tRNA/sup Phe/(E.coli) and tRNA/sup Arg/(E. coli) but not in the other species of tRNAs examined. Several hypotheses to explain this observation are discussed.

  11. Augmentation of protein production by a combination of the T7 RNA polymerase system and ubiquitin fusion: Overproduction of the human DNA repair protein, ERCC1, as a ubiquitin fusion protein in Escherichia coli.

    NARCIS (Netherlands)

    M.H.M. Koken (Marcel); J.H. Odijk; M. van Duin (Mark); M.W.J. Fornerod (Maarten); D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan)

    1993-01-01

    textabstractThis article presents the development of a set of new expression vectors for overproduction of proteins in Escherichia coli. The vectors, pETUBI-ES1, 2 and 3, allow in-frame cloning of any sequence with the ubiquitin gene driven by the strong T7f10 promoter. Combination of the T7

  12. Melibiose permease and alpha-galactosidase of Escherichia coli: Identification by selective labeling using a T7 RNA polymerase/promoter expression system

    International Nuclear Information System (INIS)

    Pourcher, T.; Bassilana, M.; Sarkar, H.K.; Kaback, H.R.; Leblanc, G.

    1990-01-01

    Identification and selective labeling of the melibiose permease and alpha-galactosidase in Escherichia coli, which are encoded by the melB and melA genes, respectively, have been accomplished by selectively labeling the two gene products with a T7 RNA polymerase expression system. Following generation of a novel EcoRI restriction site in the intergenic sequence between the two genes of the mel operon by oligonucleotide-directed, site-specific mutagenesis, melA and melB were separately inserted into plasmid pT7-6 of the T7 expression system. Expression of melB was markedly enhanced by placing a strong, synthetic ribosome binding site at an optimal distance upstream from the initiation codon of melB. Expression of cloned gene products was characterized functionally and by performing autoradiographic analysis on total cell, inner membrane, and cytoplasmic proteins from cells pulse labeled with (35S)methionine in the presence of rifampicin and resolved by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The results first confirm that alpha-galactosidase is a cytoplasmic protein with an Mr of 50K; in contrast, the membrane-bound melibiose permease is identified as a protein with an apparent Mr of 39K, a value significantly higher than that of 30K previously suggested

  13. Leakage of Intracellular UV Materials of High Hydrostatic Pressure-Injured Escherichia Coli O157:H7 Strains in Tomato Juice

    Science.gov (United States)

    The effect of high hydrostatic pressure (HHP) treatment on inactivation, injury and recovery of Salmonella Enteritidis and Escherichia coli O157:H7 cocktail inoculated in tomato juice (pH 4.1) and phosphate buffer saline (PBS. pH 7.2) at 8.0 log CFU/ml and treated at 350, 400, 450 MPa for 20 min at ...

  14. 29 CFR 1905.7 - Form of documents; subscription; copies.

    Science.gov (United States)

    2010-07-01

    ... UNDER THE WILLIAMS-STEIGER OCCUPATIONAL SAFETY AND HEALTH ACT OF 1970 General § 1905.7 Form of documents... 29 Labor 5 2010-07-01 2010-07-01 false Form of documents; subscription; copies. 1905.7 Section 1905.7 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION...

  15. Plasmid profile of Escherichia coli 0157:H7 from apparently healthy ...

    African Journals Online (AJOL)

    One hundred samples from healthy animals were screened for the presence of enterohaemorrhagic Escherichia coli 0157: H7 and 17 were positive for EHEC 0157:H7 after confirmation using serology kits. Antibiotic susceptibility patterns showed the isolates to be highly susceptible to the various antibiotics screened with a ...

  16. Quantification of plasmid DNA reference materials for Shiga toxin-producing Escherichia coli based on UV, HR-ICP-MS and digital PCR.

    Science.gov (United States)

    Liang, Wen; Xu, Li; Sui, Zhiwei; Li, Yan; Li, Lanying; Wen, Yanli; Li, Chunhua; Ren, Shuzhen; Liu, Gang

    2016-01-01

    The accuracy and metrology traceability of DNA quantification is becoming a critical theme in many fields, including diagnosis, forensic analysis, microorganism detection etc. Thus the research of DNA reference materials (RMs) and consistency of DNA quantification methods has attracted considerable research interest. In this work, we developed 3 plasmid candidate RMs, containing 3 target genes of Escherichia coli O157:H7 (E. coli O157:H7) and other Shiga toxin-producing Escherichia coli (STEC): stx1, stx2, and fliC (h7) respectively. Comprehensive investigation of the plasmid RMs was performed for their sequence, purity, homogeneity and stability, and then the concentration was quantified by three different methods: ultraviolet spectrophotometer (UV), high resolution inductively coupled plasma mass spectrometry (HR-ICP-MS) and digital PCR. As a routinely applied method for DNA analysis, UV was utilized for the quantification (OD260) and purity analysis for the plasmids. HR-ICP-MS quantified the plasmid DNA through analysing the phosphorus in DNA molecules. Digital PCR distributed the DNA samples onto a microarray chip containing thousands of reaction chambers, and quantified the DNA copy numbers by analysing the number of positive signals without any calibration curves needed. Based on the high purification of the DNA reference materials and the optimization of dPCR analysis, we successfully achieved good consistency between UV, HR-ICP-MS and dPCR, with relative deviations lower than 10 %. We then performed the co-quantification of 3 DNA RMs with three different methods together, and the uncertainties of their concentration were evaluated. Finally, the certified values and expanded uncertainties for 3 DNA RMs (pFliC, pStx1 and pStx2) were (1.60 ± 0.10) × 10(10) copies/μL, (1.53 ± 0.10) × 10(10) copies/μL and (1.70 ± 0.11) × 10(10) copies/μL respectively.Graphical abstractWe developed 3 plasmid candidate RMs, containing 3 target genes of

  17. Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control.

    Science.gov (United States)

    Baumschlager, Armin; Aoki, Stephanie K; Khammash, Mustafa

    2017-11-17

    Light has emerged as a control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark state, high expression strength when induced with blue light, and an inducible range of more than 300-fold. Following optimization of the system to reduce expression variability, we created a variant that returns to the inactive dark state within minutes once the blue light is turned off. This allows for precise dynamic control of gene expression, which is a key aspect for most applications using optogenetic regulation. The regulators, which only require blue light from ordinary light-emitting diodes for induction, were developed and tested in the bacterium Escherichia coli, which is a crucial cell factory for biotechnology due to its fast and inexpensive cultivation and well understood physiology and genetics. Opto-T7RNAP, with minor alterations, should be extendable to other bacterial species as well as eukaryotes such as mammalian cells and yeast in which the T7 RNA polymerase and the light-inducible Vivid regulator have been shown to be functional. We anticipate that our approach will expand the applicability of using light as an inducer for gene expression independent from cellular regulation and allow for a more reliable dynamic control of synthetic and natural gene networks.

  18. Thioredoxin from Escherichia coli

    International Nuclear Information System (INIS)

    Holmgren, A.; Ohlsson, I.; Grankvist, M.L.

    1978-01-01

    A competition radioimmunoassay for Escherichia coli thioredoxin using 125 I-labeled thioredoxin-S 2 and a double antibody technique was developed. The method permits determination of picomole amounts of thioredoxin in crude cell extracts and was used to study the localization of thioredoxin cell fractions. E. coli B was calculated to have approximately 10,000 copies of thioredoxin per cell mainly located in the soluble fraction after separation of the membrane and soluble fractions by gentle lysis and centrifugation. E. coli B tsnC mutants which are defective in the replication of phage T7 DNA in vivo and in vitro were examined for their content of thioredoxin. E. coli B tsnC 7004 contained no detectable level of thioredoxin in cell-free extracts examined under a variety of conditions. The results strongly suggest that tsnC 7004 is a nonsense or deletion mutant. Two other E. coli tsnC mutants, 7007 and 7008, contained detectable levels of thioredoxin in crude extracts as measured by thioredoxin reductase and gave similar immunoprecipitation reactions as the parent strain B/1. By radioimmunoassay incompletely cross-reacting material was present in both strains. These results show that tsnC 7007 and 7008 belong to a type of thioredoxin mutants with missence mutations in the thioredoxin gene affecting the function of thioredoxin as subunit in phage T7 DNA polymerase

  19. Cellular localization of the Escherichia coli SpoT protein.

    OpenAIRE

    Gentry, D R; Cashel, M

    1995-01-01

    The SpoT protein of Escherichia coli serves as a source of degradation as well as an apparent source of synthesis of (p)ppGpp. Since the subcellular localization of SpoT might be a clue to its function, we have used SpoT-specific antisera to analyze cell extracts fractionated on sucrose gradients. We find that the SpoT protein is not bound to ribosomes or to either inner or outer membrane fractions. Although the SpoT protein is found in large aggregates, its localization is probably cytosolic.

  20. Expression of the N2 fixation gene operon of Paenibacillus sp. WLY78 under the control of the T7 promoter in Escherichia coli BL21.

    Science.gov (United States)

    Zhang, Lihong; Liu, Xiaomeng; Li, Xinxin; Chen, Sanfeng

    2015-10-01

    To investigate the transcription and translation and nitrogenase activity of the nine N2-fixing-gene (nif) operon (nifBHDKENXhesAnifX) of Paenibacillus sp. WLY78 under the control of the T7 promoter in Escherichia coli BL21 under different conditions. The Paenibacillus nif operon under the control of the T7 promoter is significantly transcribed and effectively translated in E. coli BL21 when grown in medium containing organic N compounds (yeast extract and Tryptone) or NH4+ by using RT-PCR and Western blot analysis. Transcription and translation of foreign nif genes in E. coli are not inhibited by environmental organic or inorganic N compounds or O2. However, contrary to transcription and translation, nitrogenase activity is 4% lower in the recombinant E. coli 78-32 compared to the native Paenibacillus sp. WLY78. The Paenibacillus nif operon under the control of T7 promoter enables E. coli BL21 to synthesize active nitrogenase. This study shows how the nif gene operon can be transferred to non-N2-fixing bacteria or to eukaryotic organelles.

  1. D10 value determination for Escherichia coli O157:H7 in different cultivations

    International Nuclear Information System (INIS)

    Oliveira, Sergio Eduardo M. de; Pires, Luis Fernando G.; Vital, Helio de C.

    2002-01-01

    Escherichia coli serum type O157:H7 is a highly pathogenic bacterium. Inside the human body, that microorganism causes a disease that leads to bloody diarrhea, stoppage of kidney functions and clots in the brain. That type of infection has been related to the consumption of different varieties of foods, mainly meat and other products of animal origin. Irradiation is an efficient method for elimination of pathogenic and spoiling microorganisms in foods. Thus, this work investigates the use of gamma irradiation for elimination of Escherichia coli O157:H7. For that purpose, inoculated samples in trypticase soy broth and saline solution 0,85% media were exposed to several gamma radiation doses. Counting the number of surviving bacteria yielded the following D 10 values for Escherichia coli O157:H7: 98±7 Gy, in trypticase soy broth and 49±4 Gy in saline solution 0,85% medium. (author)

  2. Lethality prediction for Escherichia coli 0157:H7 and Uropathogenic E. coli in ground chicken treated with high pressure processing and trans-cinnamaldehyde

    Science.gov (United States)

    Pathogenic Escherichia coli, intestinal (O157:H7) as well as extraintestinal types (Uropathogenic E. coli (UPEC)) are commonly found in many foods including chicken meat. In this study we compared the resistance of E. coli O157:H7 to UPEC in chicken meat under the stresses of high hydrostatic pressu...

  3. Escherichia coli tRNAArg acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis

    International Nuclear Information System (INIS)

    Eichert, André; Schreiber, Angela; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

    2009-01-01

    Various E. coli tRNA Arg acceptor-stem microhelix isoacceptors have been crystallized and investigated by high-resolution X-ray diffraction analysis. The aminoacylation of tRNA is a crucial step in cellular protein biosynthesis. Recognition of the cognate tRNA by the correct aminoacyl-tRNA synthetase is ensured by tRNA identity elements. In tRNA Arg , the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the aminoacyl stem interacts with the arginyl-tRNA synthetase. As a consequence of the redundancy of the genetic code, six tRNA Arg isoacceptors exist. In the present work, three different Escherichia coli tRNA Arg acceptor-stem helices were crystallized. Two of them, the tRNA Arg microhelices RR-1660 and RR-1662, were examined by X-ray diffraction analysis and diffracted to 1.7 and 1.8 Å resolution, respectively. The tRNA Arg RR-1660 helix crystallized in space group P1, with unit-cell parameters a = 26.28, b = 28.92, c = 29.00 Å, α = 105.74, β = 99.01, γ = 97.44°, whereas the tRNA Arg RR-1662 helix crystallized in space group C2, with unit-cell parameters a = 33.18, b = 46.16, c = 26.04 Å, β = 101.50°

  4. 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.

  5. Identification of chloroquine resistance Pfcrt-K76T and determination of Pfmdr1-N86Y copy number by SYBR Green I qPCR

    Directory of Open Access Journals (Sweden)

    Addimas Tajebe

    2015-03-01

    Conclusions: The study showed high prevalence level and fixation of Pfcrt, 76T mutation after chloroquine withdrawal. The prevalence of Pfmdr1 copy number variant suggested that the presence of modulating factor for emergence of Plasmodium falciparum strains with higher copy numbers. However, the prevalence level was not statistically significant.

  6. Cloning and expression of the Escherichia coli K-12 sad gene.

    OpenAIRE

    Marek, L E; Henson, J M

    1988-01-01

    The Escherichia coli K-12 sad gene, which encodes an NAD-dependent succinic semialdehyde dehydrogenase, was cloned into a high-copy-number vector. Minicells carrying a sad+ plasmid produced a 55,000-dalton peptide, the probable sad gene product.

  7. Involvement of DNA gyrase in replication and transcription of bacteriophage T7 DNA

    International Nuclear Information System (INIS)

    De Wyngaert, M.A.; Hinkle, D.C.

    1979-01-01

    Growth of bacteriophage T7 is inhibited by the antibiotic coumermycin A 1 , an inhibitor of the Escherichia coli DNA gyrase. Since growth of the phage is insensitive to the antibiotic in strains containing a coumermycin-resistent DNA gyrase, this enzyme appears to be required for phage growth. We have investigated the effect of coumermycin on the kinetics of DNA, RNA, and protein synthesis during T7 infection. DNA synthesis is completely inhibited by the antibiotic. In addition, coumermycin significantly inhibits transcription of late but not early genes. Thus, E. coli DNA gyrase may play an important role in transcription as well as in replication of T7 DNA

  8. 18 CFR 34.7 - Number of copies to be filed.

    Science.gov (United States)

    2010-04-01

    ..., § 34.7 was revised, effective at the time of the next e-filing release during the Commission's next fiscal year. For the convenience of the user, the revised text follows: § 34.7 Filing requirements. Each...) and (2) of this chapter. As a qualified document, no paper copy version of the filing is required...

  9. the occurrence of escherichia coli o157:h7 in market and abattoir

    African Journals Online (AJOL)

    user

    Escherichia coli O157:H7 is a newly emerging pathogen frequently associated with the consumption of foods of ... KEY WORDS: E. coli O157:H7, Pathogen, Abattoir, Market, and Infections ..... pathogen. Escherichia coli O157:H7 as a model of.

  10. High-resolution T{sub 2}-weighted cervical cancer imaging: a feasibility study on ultra-high-field 7.0-T MRI with an endorectal monopole antenna

    Energy Technology Data Exchange (ETDEWEB)

    Hoogendam, Jacob P.; Verheijen, Rene H.M.; Zweemer, Ronald P. [University Medical Centre Utrecht, Department of Gynaecological Oncology, UMC Utrecht Cancer Centre, PO Box 85500, Utrecht (Netherlands); Kalleveen, Irene M.L.; Castro, Catalina S.A. de; Raaijmakers, Alexander J.E.; Bosch, Maurice A.A.J. van den; Klomp, Dennis W.J.; Veldhuis, Wouter B. [University Medical Centre Utrecht, Department of Radiology, Utrecht (Netherlands)

    2017-03-15

    We studied the feasibility of high-resolution T{sub 2}-weighted cervical cancer imaging on an ultra-high-field 7.0-T magnetic resonance imaging (MRI) system using an endorectal antenna of 4.7-mm thickness. A feasibility study on 20 stage IB1-IIB cervical cancer patients was conducted. All underwent pre-treatment 1.5-T MRI. At 7.0-T MRI, an external transmit/receive array with seven dipole antennae and a single endorectal monopole receive antenna were used. Discomfort levels were assessed. Following individualised phase-based B{sub 1} {sup +} shimming, T{sub 2}-weighted turbo spin echo sequences were completed. Patients had stage IB1 (n = 9), IB2 (n = 4), IIA1 (n = 1) or IIB (n = 6) cervical cancer. Discomfort (ten-point scale) was minimal at placement and removal of the endorectal antenna with a median score of 1 (range, 0-5) and 0 (range, 0-2) respectively. Its use did not result in adverse events or pre-term session discontinuation. To demonstrate feasibility, T{sub 2}-weighted acquisitions from 7.0-T MRI are presented in comparison to 1.5-T MRI. Artefacts on 7.0-T MRI were due to motion, locally destructive B{sub 1} interference, excessive B{sub 1} under the external antennae and SENSE reconstruction. High-resolution T{sub 2}-weighted 7.0-T MRI of stage IB1-IIB cervical cancer is feasible. The addition of an endorectal antenna is well tolerated by patients. (orig.)

  11. 36 CFR 1012.7 - Can I get an authenticated copy of a Presidio Trust record?

    Science.gov (United States)

    2010-07-01

    ... copy of a Presidio Trust record, for purposes of admissibility under Federal, State or Tribal law. We... copy of a Presidio Trust record? 1012.7 Section 1012.7 Parks, Forests, and Public Property PRESIDIO TRUST LEGAL PROCESS: TESTIMONY BY EMPLOYEES AND PRODUCTION OF RECORDS Responsibilities of Requesters...

  12. Modeling the inactivation of Escherichia coli 0157:H7 and uropathogenic E.coli in ground chicken by high pressure processing and thymol

    Science.gov (United States)

    Disease causing Escherichia coli commonly found in meat and poultry include intestinal pathogenic E. coli (iPEC) as well as extraintestinal types such as the Uropathogenic E. coli (UPEC). In this study we compare the resistance of iPEC (O157:H7) to UPEC in chicken meat using High Pressure Processing...

  13. Modeling the inactivatin of Escherichia coli 0157:H7 and uropathogenic E. coli in ground beef by high pressure processing and citral

    Science.gov (United States)

    Disease causing Escherichia coli commonly found in meat and poultry include intestinal pathogenic E. coli (iPEC) as well as extraintestinal types such as the Uropathogenic E. coli (UPEC). In this study we compared the resistance of iPEC (O157:H7) to UPEC in ground beef using High Pressure Processing...

  14. Feasibility of using ultra-high field (7 T MRI for clinical surgical targeting.

    Directory of Open Access Journals (Sweden)

    Yuval Duchin

    Full Text Available The advantages of ultra-high magnetic field (7 Tesla MRI for basic science research and neuroscience applications have proven invaluable. Structural and functional MR images of the human brain acquired at 7 T exhibit rich information content with potential utility for clinical applications. However, (1 substantial increases in susceptibility artifacts, and (2 geometrical distortions at 7 T would be detrimental for stereotactic surgeries such as deep brain stimulation (DBS, which typically use 1.5 T images for surgical planning. Here, we explore whether these issues can be addressed, making feasible the use of 7 T MRI to guide surgical planning. Twelve patients with Parkinson's disease, candidates for DBS, were scanned on a standard clinical 1.5 T MRI and a 7 T MRI scanner. Qualitative and quantitative assessments of global and regional distortion were evaluated based on anatomical landmarks and transformation matrix values. Our analyses show that distances between identical landmarks on 1.5 T vs. 7 T, in the mid-brain region, were less than one voxel, indicating a successful co-registration between the 1.5 T and 7 T images under these specific imaging parameter sets. On regional analysis, the central part of the brain showed minimal distortion, while inferior and frontal areas exhibited larger distortion due to proximity to air-filled cavities. We conclude that 7 T MR images of the central brain regions have comparable distortions to that observed on a 1.5 T MRI, and that clinical applications targeting structures such as the STN, are feasible with information-rich 7 T imaging.

  15. Identification and Prevalence of Escherichia coli and Escherichia coli O157: H7 in Foods

    Directory of Open Access Journals (Sweden)

    Ancuta Mihaela Rotar

    2013-11-01

    Full Text Available The objective of this study is to investigate the incidence of Escherichia coli in animal and non-animal foods, and mainly the incidence of the serotype O157: H7 producing verotoxin. The presence of common Escherichia coli and Escherichia coli O157: H7 in various foods (of animal and non animal origin was performed in Transylvania area. We analyzed a total of one hundred forty-one samples of minced meat, one hundred twenty-six samples of meat , twenty six samples of meat products, five samples of alcoholic beverages, three samples of seafood, one hundred samples of cheese from pasteurized milk, seventeen samples of butter, four samples of vegetables and one sample of milk powder, using the standard cultural method and Vidas Eco method for E. coli O157: H7 strains. E. coli was identified in 50 samples of minced meat, 55 samples of meat prepared, 4 samples of meat products, 2 samples of alcoholic beverages, 25 samples of cheese from pasteurized milk, 6 samples of butter and 1 sample of vegetables. In this study were not been identified any foods contaminated with the E. coli O157: H7 serotype. The results of this reasearch have demostrated that E. coli wich represents a hygienic indicator of recent food contamination, can be destroyed with heat treatment and hygienic handling of foods. Our country over the years has been among the few countries where the incidence of the E. coli O157: H7 serotype has been minimal.

  16. Mechanosensing regulates virulence in Escherichia coli O157:H7.

    Science.gov (United States)

    Islam, Md Shahidul; Krachler, Anne Marie

    2016-01-01

    Enterohemorrhagic Escherichia coli O157:H7 is a food-borne pathogen transmitted via the fecal-oral route, and can cause bloody diarrhea and hemolytic uremic syndrome (HUS) in the human host. Although a range of colonization factors, Shiga toxins and a type III secretion system (T3SS) all contribute to disease development, the locus of enterocyte effacement (LEE) encoded T3SS is responsible for the formation of lesions in the intestinal tract. While a variety of chemical cues in the host environment are known to up-regulate LEE expression, we recently demonstrated that changes in physical forces at the site of attachment are required for localized, full induction of the system and thus spatial regulation of virulence in the intestinal tract. Here, we discuss our findings in the light of other recent studies describing mechanosensing of the host and force-dependent induction of virulence mechanisms. We discuss potential mechanisms of mechanosensing and mechanotransduction, and the level of conservation across bacterial species.

  17. Specific structural probing of plasmid-coded ribosomal RNAs from Escherichia coli

    DEFF Research Database (Denmark)

    Aagaard, C; Rosendahl, G; Dam, M

    1991-01-01

    The preferred method for construction and in vivo expression of mutagenised Escherichia coli ribosomal RNAs (rRNAs) is via high copy number plasmids. Transcription of wild-type rRNA from the seven chromosomal rrn operons in strains harbouring plasmid-coded mutant rRNAs leads to a heterogeneous...

  18. The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ0 Transport

    Directory of Open Access Journals (Sweden)

    Rémi Zallot

    2017-02-01

    Full Text Available Queuosine (Q is a complex modification of the wobble base in tRNAs with GUN anticodons. The full Q biosynthesis pathway has been elucidated in Escherichia coli. FolE, QueD, QueE and QueC are involved in the conversion of guanosine triphosphate (GTP to 7-cyano-7-deazaguanine (preQ0, an intermediate of increasing interest for its central role in tRNA and DNA modification and secondary metabolism. QueF then reduces preQ0 to 7-aminomethyl-7-deazaguanine (preQ1. PreQ1 is inserted into tRNAs by tRNA guanine(34 transglycosylase (TGT. The inserted base preQ1 is finally matured to Q by two additional steps involving QueA and QueG or QueH. Most Eubacteria harbor the full set of Q synthesis genes and are predicted to synthesize Q de novo. However, some bacteria only encode enzymes involved in the second half of the pathway downstream of preQ0 synthesis, including the signature enzyme TGT. Different patterns of distribution of the queF, tgt, queA and queG or queH genes are observed, suggesting preQ0, preQ1 or even the queuine base being salvaged in specific organisms. Such salvage pathways require the existence of specific 7-deazapurine transporters that have yet to be identified. The COG1738 family was identified as a candidate for a missing preQ0/preQ1 transporter in prokaryotes, by comparative genomics analyses. The existence of Q precursor salvage was confirmed for the first time in bacteria, in vivo, through an indirect assay. The involvement of the COG1738 in salvage of a Q precursor was experimentally validated in Escherichia coli, where it was shown that the COG1738 family member YhhQ is essential for preQ0 transport.

  19. Ultra high spatial and temporal resolution breast imaging at 7T.

    Science.gov (United States)

    van de Bank, B L; Voogt, I J; Italiaander, M; Stehouwer, B L; Boer, V O; Luijten, P R; Klomp, D W J

    2013-04-01

    There is a need to obtain higher specificity in the detection of breast lesions using MRI. To address this need, Dynamic Contrast-Enhanced (DCE) MRI has been combined with other structural and functional MRI techniques. Unfortunately, owing to time constraints structural images at ultra-high spatial resolution can generally not be obtained during contrast uptake, whereas the relatively low spatial resolution of functional imaging (e.g. diffusion and perfusion) limits the detection of small lesions. To be able to increase spatial as well as temporal resolution simultaneously, the sensitivity of MR detection needs to increase as well as the ability to effectively accelerate the acquisition. The required gain in signal-to-noise ratio (SNR) can be obtained at 7T, whereas acceleration can be obtained with high-density receiver coil arrays. In this case, morphological imaging can be merged with DCE-MRI, and other functional techniques can be obtained at higher spatial resolution, and with less distortion [e.g. Diffusion Weighted Imaging (DWI)]. To test the feasibility of this concept, we developed a unilateral breast coil for 7T. It comprises a volume optimized dual-channel transmit coil combined with a 30-channel receive array coil. The high density of small coil elements enabled efficient acceleration in any direction to acquire ultra high spatial resolution MRI of close to 0.6 mm isotropic detail within a temporal resolution of 69 s, high spatial resolution MRI of 1.5 mm isotropic within an ultra high temporal resolution of 6.7 s and low distortion DWI at 7T, all validated in phantoms, healthy volunteers and a patient with a lesion in the right breast classified as Breast Imaging Reporting and Data System (BI-RADS) IV. Copyright © 2012 John Wiley & Sons, Ltd.

  20. Cellular damage of Escherichia coli 0157:H7 and Salmonella spp. in apple juice treated with high hydrostatic pressure and thermal death time disks

    Science.gov (United States)

    Differences in membrane damage including leakage of intracellular UV-materials and loss of viability of Salmonella spp. and Escherichia coli O157:H7 bacteria in apple juice, pH 3.1 following thermal-death-time (TDT) disk and high hydrostatic pressure (HHP) treatments were investigated. Salmonella an...

  1. Repair of damage induced by ultraviolet radiation in mutator T-1 Escherichia coli transductants

    International Nuclear Information System (INIS)

    Sideropoulos, A.S.; Greenberg, J.; Warren, G.

    1975-01-01

    To ascertain whether a relationship commonly exists between azide resistance, ultraviolet (uv) resistance, and the mutator property (mut T-1), we performed uv survival and mutation frequency determinations with and without caffeine (2.571 mM) in nonmutator azide resistant (azi/sup r/) and phage mediated mut T-1 transductants of Escherichia coli K-12, B/r, B/r T-, Bs-1, and Bs-8. The strains constructed were assumed to be ''co-isogenic'' except for the mutator factor. The frequency of mutation to streptomycin resistance (str/sup r/) was relatively constant and approximated 2 x 10- 7 . Transductants carrying the azide marker with or without the mut T-1 gene had the same level of uv survival as the parent with the same mutator phenotype. Dark repair of the prelethal uv lesion is equally caffeine sensitive in the nonmutator and mutator HCR+ strains. Our results indicated that the mut T-1 strains possess an efficient dark repair system for uv damage and that the mechanism of mut T-1 action is independent of uv dark repair processes. (auth)

  2. Increased riboflavin production by knockout of 6-phosphofructokinase I and blocking the Entner-Doudoroff pathway in Escherichia coli.

    Science.gov (United States)

    Liu, Shuang; Kang, Pei; Cui, Zhenzhen; Wang, Zhiwen; Chen, Tao

    2016-08-01

    To construct an Escherichia coli strain capable of producing riboflavin with high titer and yield. A low copy number plasmid pLS01 containing a riboflavin operon under the control of a constitutive promoter was constructed and introduced into Escherichia coli MG1655. Subsequently, the pfkA, edd and ead genes were disrupted, and the resulting strain LS02T produced 667 mg riboflavin/l in MSY medium supplied with 10 g glucose/l in flask cultivation. In a fed-batch process, riboflavin production of the strain reached 10.4 g/l with a yield of 56.8 mg riboflavin/g glucose. To our knowledge, this is the first report of engineered E. coli strains that can produce more than 10 g riboflavin/l in fed-batch cultivation, indicating that E. coli has potential for riboflavin production.

  3. Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids

    Directory of Open Access Journals (Sweden)

    Ward Jordan D

    2008-08-01

    Full Text Available Abstract Background Many microbes possess restriction-modification systems that protect them from parasitic DNA molecules. Unfortunately, the presence of a restriction-modification system in a given microbe also hampers genetic analysis. Although plasmids can be successfully conjugated into the enteropathogenic Escherichia coli strain E2348/69 and optimized protocols for competent cell preparation have been developed, we found that a large, low copy (~15 bioluminescent reporter plasmid, pJW15, that we modified for use in EPEC, was exceedingly difficult to transform into E2348/69. We reasoned that a restriction-modification system could be responsible for the low transformation efficiency of E2348/69 and sought to identify and inactivate the responsible gene(s, with the goal of creating an easily transformable strain of EPEC that could complement existing protocols for genetic manipulation of this important pathogen. Results Using bioinformatics, we identified genes in the unfinished enteropathogenic Escherichia coli (EPEC strain E2348/69 genome whose predicted products bear homology to the HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type I restriction-modification systems. We constructed a strain carrying a deletion of the conserved enzymatic domain of the EPEC HsdR homologue, NH4, and showed that its transformation efficiency was up to four orders of magnitude higher than that of the parent strain. Further, the modification capacity of NH4 remained intact, since plasmids that were normally recalcitrant to transformation into E2348/69 could be transformed upon passage through NH4. NH4 was unaffected in virulence factor production, since bundle forming pilus (BFP subunits and type III secreted (T3S proteins were present at equivalent levels to those seen in E2348/69. Further, NH4 was indistinguishable from E2348/69 in tissue culture infection model assays of localized adherence and T3S. Conclusion We

  4. Radiosensitivity of the induction of early enzymes by. gamma. -irradiated T7-phages

    Energy Technology Data Exchange (ETDEWEB)

    Bopp, E

    1975-01-01

    The radiosensitivity of the ability of the bacteriophage T7 to produce polymerase and lysozyme during its reproduction cycle is investigated. B-cells of Escherichia coli were infected with /sup 60/Co-..gamma..-irradiated T7 phages. From the extracts of the cells opened by ultrasonic waves, the amount of enzymes produced is determined with the aid of special enzyme tests. The fraction of inactivated phages able to produce RNA polymerase is higher than the fraction with intact DNA double strands and higher than the fraction able to inject DNA. The lowest fraction is that of inactivated phages producing lysozyme.

  5. Affinity labeling of Escherichia coli phenylalanyl-tRNA synthetase at the binding site for tRNA

    International Nuclear Information System (INIS)

    Hountondji, C.; Schmitter, J.M.; Beauvallet, C.; Blanquet, S.

    1987-01-01

    Periodate-oxidized tRNA/sup Phe/ (tRNA/sub ox//sup Phe/) behaves as a specific affinity label of tetrameric Escherichia coli phenylalanyl-tRNA synthetase (PheRS). Reaction of the α 2 β 2 enzyme with tRNA/sub ox//sup Phe/ results in the loss of tRNA/sup Phe/ aminoacylation activity with covalent attachment of 2 mol of tRNA dialdehyde/mol of enzyme, in agreement with the stoichiometry of tRNA binding. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the PheRS-[ 14 C]tRNA/sub ox//sup Phe/ covalent complex indicates that the large (α, M/sub r/ 87K) subunit of the enzyme interacts with the 3'-adenosine of tRNA/sub ox//sup Phe/. The [ 14 C]tRNA-labeled chymotryptic peptides of PheRS were purified by both gel filtration and reverse-phase high-performance liquid chromatography. The radioactivity was almost equally distributed among three peptides: Met-Lys[Ado]-Phe, Ala-Asp-Lys[Ado]-Leu, and Lys-Ile-Lys[Ado]-Ala. These sequences correspond to residues 1-3, 59-62, and 104-107, respectively, in the N-terminal region of the 795 amino acid sequence of the α subunit. It is noticeable that the labeled peptide Ala-Asp-Lys-Leu is adjacent to residues 63-66 (Arg-Val-Thr-Lys). The latter sequence was just predicted to resemble the proposed consensus tRNA CCA binding region Lys-Met-Ser-Lys-Ser, as deduced from previous affinity labeling studies on E. coli methionyl- and tyrosyl-tRNA synthetases

  6. High-resolution whole-brain diffusion MRI at 7T using radiofrequency parallel transmission.

    Science.gov (United States)

    Wu, Xiaoping; Auerbach, Edward J; Vu, An T; Moeller, Steen; Lenglet, Christophe; Schmitter, Sebastian; Van de Moortele, Pierre-François; Yacoub, Essa; Uğurbil, Kâmil

    2018-03-30

    Investigating the utility of RF parallel transmission (pTx) for Human Connectome Project (HCP)-style whole-brain diffusion MRI (dMRI) data at 7 Tesla (7T). Healthy subjects were scanned in pTx and single-transmit (1Tx) modes. Multiband (MB), single-spoke pTx pulses were designed to image sagittal slices. HCP-style dMRI data (i.e., 1.05-mm resolutions, MB2, b-values = 1000/2000 s/mm 2 , 286 images and 40-min scan) and data with higher accelerations (MB3 and MB4) were acquired with pTx. pTx significantly improved flip-angle detected signal uniformity across the brain, yielding ∼19% increase in temporal SNR (tSNR) averaged over the brain relative to 1Tx. This allowed significantly enhanced estimation of multiple fiber orientations (with ∼21% decrease in dispersion) in HCP-style 7T dMRI datasets. Additionally, pTx pulses achieved substantially lower power deposition, permitting higher accelerations, enabling collection of the same data in 2/3 and 1/2 the scan time or of more data in the same scan time. pTx provides a solution to two major limitations for slice-accelerated high-resolution whole-brain dMRI at 7T; it improves flip-angle uniformity, and enables higher slice acceleration relative to current state-of-the-art. As such, pTx provides significant advantages for rapid acquisition of high-quality, high-resolution truly whole-brain dMRI data. © 2018 International Society for Magnetic Resonance in Medicine.

  7. Purification and properties of poliovirus RNA polymerase expressed in Escherichia coli

    International Nuclear Information System (INIS)

    Plotch, S.J.; Palant, O.; Gluzman, Y.

    1989-01-01

    A cDNA clone encoding the RNA polymerase of poliovirus has been expressed in Escherichia coli under the transcriptional control of a T7 bacteriophage promoter. This poliovirus enzyme was designed to contain only a single additional amino acid, the N-terminal methionine. The recombinant enzyme has been purified to near homogeneity, and polyclonal antibodies have been prepared against it. The enzyme exhibits poly(A)-dependent oligo(U)-primed ply(U) polymerase activity as well as RNA polymerase activity. In the presence of an oligo(U) primer, the enzyme catalyzes the synthesis of a full-length copy of either poliovirus or globin RNA templates. In the absence of added primer, RNA products up to twice the length of the template are synthesized. When incubated in the presence of a single nucleoside triphosphate, [α- 32 P]UTP, the enzyme catalyzes the incorporation of radioactive label into template RNA. These results are discussed in light of previously proposed models of poliovirus RNA synthesis in vitro

  8. Escherichia coli O157:H7 - An Emerging Pathogen in foods of Animal Origin

    Directory of Open Access Journals (Sweden)

    Ch. Bindu Kiranmayi

    Full Text Available Escherichia coli O157:H7 is an emerging public health concern in most countries of the world. E. coli O157:H7 was known to be a human pathogen for nearly 24 years. EHEC O157 infection is estimated to be the fourth most costly food borne disease in Canada and USA, not counting the cost of possible litigation. E. coli O157:H7 and Salmonella are the leading causes of produce related outbreaks, accounting for 20 and 30% respectively. The authority of the Federal Meat Inspection Act, FSIS (Food Safety and Inspection Service declared Escherichia coli O157:H7, an adulterant in raw ground beef and enforced “zero tolerance” (USDA-FSIS, 17 December 1998. Because of the severity of these illnesses and the apparent low infective dose (less than 10 cells, Escherichia coli O157:H7 is considered one of the most serious of known food borne pathogens. Escherichia coli O157:H7 is mainly pathogenic to human but in cattle and other animals, it did not induce any clinical disease except diarrhea. So, these animals act as carriers to Escherichia coli O157:H7. The majority transmission is through eating of undercooked contaminated ground meat and consumption of raw milk, raw vegetables, fruits contaminated by water, cheese, curd and also through consumption of sprouts, lettuce and juice. The conventional isolation procedure includes growth in enrichment broth like modified EC (E. coli broth or modified tryptic soy broth (mTSB Since the infection primarily occurs via faeco-oral route, the preventive measures include food hygiene measures like proper cooking of meat, consumption of pasteurized milk, washing fruits and vegetables especially those to be eaten raw and drinking chlorine treated water and personnel hygiene measures like washing hands after toilet visits. [Veterinary World 2010; 3(8.000: 382-389

  9. The Development of a Portable SPR Bioanalyzer for Sensitive Detection of Escherichia coli O157:H7

    Directory of Open Access Journals (Sweden)

    Shun Wang

    2016-11-01

    Full Text Available The purpose of this study was to develop a portable surface plasmon resonance (SPR bioanalyzer for the sensitive detection of Escherichia coli O157:H7 in comparison with an enzyme-linked immunosorbent assay (ELISA. The experimental setup mainly consisted of an integrated biosensor and a homemade microfluidic cell with a three-way solenoid valve. In order to detect Escherichia coli O157:H7 using the SPR immunoassay, 3-mercaptopropionic acid (3-MPA was chemisorbed onto a gold surface via covalent bond for the immobilization of biological species. 1-ethyl-3-(3-dimethylaminopropyl carbodiimide hydrochloride (EDC and N-hydroxysuccinimide (NHS were used as crosslinker reagents to enable the reaction between 3-MPA and Escherichia coli O157:H7 antibodies by covalent –CO–NH– amide bonding. The experimental results were obtained from the Escherichia coli O157:H7 positive samples prepared by 10-, 20-, 40-, 80-, and 160-fold dilution respectively, which show that a good linear relationship with the correlation coefficient R of 0.982 existed between the response units from the portable SPR bioanalyzer and the concentration of Escherichia coli O157:H7 positive samples. Moreover, the theoretical detection limit of 1.87 × 103 cfu/mL was calculated from the positive control samples. Compared with the Escherichia coli O157:H7 ELISA kit, the sensitivity of this portable SPR bioanalyzer is four orders of magnitude higher than the ELISA kit. The results demonstrate that the portable SPR bioanalyzer could provide an alternative method for the quantitative and sensitive determination of Escherichia coli O157:H7 in field.

  10. prevalence of escherichia coli 0157:h7 in fresh and roasted beef

    African Journals Online (AJOL)

    DR. AMINU

    The prevalence of Enterohemorrhagic Escherichia coli 0157:H7 in 300 fresh beef and 150 roasted beef samples from ... likely cause of E. coli O157:H7 infection is undercooked ground beef. ..... coli O157:H7 in a sheep model. Appl. Environ.

  11. Escherichia coli O157:H7 bacteriophage 241 isolated from an industrial cucumber fermentation at high acidity and salinity

    Directory of Open Access Journals (Sweden)

    Zhongjing eLu

    2015-02-01

    Full Text Available A novel phage, 241, specific for Escherichia coli O157:H7 was isolated from an industrial cucumber fermentation where both acidity (pH  3.7 and salinity ( 5% NaCl were high. The phage belongs to the Myoviridae family. Its latent period was 15 min and average burst size was 53 phage particles per infected cell. The phage was able to lyse 48 E. coli O157:H7 strains, but none of the 18 non-O157 strains (including E. coli O104:H7 or the 2 O antigen-negative mutants of O157:H7 strain, 43895per (also lacking H7 antigen and F12 (still expressing H7 antigen. However, the phage was able to lyse a per-complemented strain (43895perComp which expresses O157 antigen. These results indicated that phage 241 is specific for O157 antigen, and E. coli strains lacking O157 antigen were resistant to the phage infection, regardless of the presence or absence of H7 antigen. SDS-PAGE profile revealed at least 13 structural proteins of the phage. The phage DNA was resistant to many commonly used restriction endonucleases, suggesting the presence of modified nucleotides in the phage genome. At the multiplicity of infection of 10, 3 or 0.3, the phage caused a rapid cell lysis within 1 or 2 h, resulting in 3.5- or 4.5-log-unit reduction in cell concentration. The high lytic activity, specificity and tolerance to low pH and high salinity make phage 241 a potentially ideal biocontrol agent of E. coli O157:H7 in various foods. To our knowledge, this is the first report on E. coli O157:H7 phage isolated from high acidity and salinity environment.

  12. High-resolution intracranial vessel wall MRI in an elderly asymptomatic population: comparison of 3T and 7T

    Energy Technology Data Exchange (ETDEWEB)

    Harteveld, Anita A.; Kolk, Anja G. van der; Dieleman, Nikki; Siero, Jeroen C.W.; Luijten, Peter R.; Zwanenburg, Jaco J.M.; Hendrikse, Jeroen [University Medical Center Utrecht, Department of Radiology, Postbox 85500, Utrecht (Netherlands); Worp, H.B. van der; Frijns, Catharina J.M. [University Medical Center Utrecht, Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht (Netherlands); Kuijf, Hugo J. [University Medical Center Utrecht, Image Sciences Institute, Utrecht (Netherlands)

    2017-04-15

    Several intracranial vessel wall sequences have been described in recent literature, with either 3-T or 7-T magnetic resonance imaging (MRI). In the current study, we compared 3-T and 7-T MRI in visualising both the intracranial arterial vessel wall and vessel wall lesions. Twenty-one elderly asymptomatic volunteers were scanned by 3-T and 7-T MRI with an intracranial vessel wall sequence, both before and after contrast administration. Two raters scored image quality, and presence and characteristics of vessel wall lesions. Vessel wall visibility was equal or significantly better at 7 T for the studied arterial segments, even though there were more artefacts hampering assessment. The better visualisation of the vessel wall at 7 T was most prominent in the proximal anterior cerebral circulation and the posterior cerebral artery. In the studied elderly asymptomatic population, 48 vessel-wall lesions were identified at 3 T, of which 7 showed enhancement. At 7 T, 79 lesions were identified, of which 29 showed enhancement. Seventy-one percent of all 3-T lesions and 59 % of all 7-T lesions were also seen at the other field strength. Despite the large variability in detected lesions at both field strengths, we believe 7-T MRI has the highest potential to identify the total burden of intracranial vessel wall lesions. (orig.)

  13. Markerless Escherichia coli rrn Deletion Strains for Genetic Determination of Ribosomal Binding Sites

    DEFF Research Database (Denmark)

    Quan, Selwyn; Skovgaard, Ole; McLaughlin, Robert E

    2015-01-01

    Single-copy rrn strains facilitate genetic ribosomal studies in Escherichia coli. Consecutive markerless deletion of rrn operons resulted in slower growth upon inactivation of the fourth copy, which was reversed by supplying transfer RNA genes encoded in rrn operons in trans. Removal of the sixth...

  14. Peer-to-peer computing for secure high performance data copying

    International Nuclear Information System (INIS)

    Hanushevsky, A.; Trunov, A.; Cottrell, L.

    2001-01-01

    The BaBar Copy Program (bbcp) is an excellent representative of peer-to-peer (P2P) computing. It is also a pioneering application of its type in the P2P arena. Built upon the foundation of its predecessor, Secure Fast Copy (sfcp), bbcp incorporates significant improvements performance and usability. As with sfcp, bbcp uses ssh for authentication; providing an elegant and simple working model--if you can ssh to a location, you can copy files to or from that location. To fully support this notion, bbcp transparently supports 3rd party copy operations. The program also incorporates several mechanism to deal with firewall security; the bane of P2P computing. To achieve high performance in a wide area network, bbcp allows a user to independently specify, the number of parallel network streams, tcp window size, and the file I/O blocking factor. Using these parameters, data is pipelined from source to target to provide a uniform traffic pattern that maximizes router efficiency. For improved recoverability, bbcp also keeps track of copy operations so that an operation can be restarted from the point of failure at a later time; minimizing the amount of network traffic in the event of a copy failure. Here, the authors present the bbcp architecture, it's various features, and the reasons for their inclusion

  15. Peer-to-Peer Computing for Secure High Performance Data Copying

    International Nuclear Information System (INIS)

    2002-01-01

    The BaBar Copy Program (bbcp) is an excellent representative of peer-to-peer (P2P) computing. It is also a pioneering application of its type in the P2P arena. Built upon the foundation of its predecessor, Secure Fast Copy (sfcp), bbcp incorporates significant improvements performance and usability. As with sfcp, bbcp uses ssh for authentication; providing an elegant and simple working model -- if you can ssh to a location, you can copy files to or from that location. To fully support this notion, bbcp transparently supports 3rd party copy operations. The program also incorporates several mechanism to deal with firewall security; the bane of P2P computing. To achieve high performance in a wide area network, bbcp allows a user to independently specify, the number of parallel network streams, tcp window size, and the file I/O blocking factor. Using these parameters, data is pipelined from source to target to provide a uniform traffic pattern that maximizes router efficiency. For improved recoverability, bbcp also keeps track of copy operations so that an operation can be restarted from the point of failure at a later time; minimizing the amount of network traffic in the event of a copy failure. Here, we preset the bbcp architecture, it's various features, and the reasons for their inclusion

  16. High-resolution anatomy of the human brain stem using 7-T MRI: improved detection of inner structures and nerves?

    Energy Technology Data Exchange (ETDEWEB)

    Gizewski, Elke R. [Medical University Innsbruck, Department of Neuroradiology, Innsbruck (Austria); Maderwald, Stefan [University Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); Linn, Jennifer; Bochmann, Katja [LMU Munich, Department of Neuroradiology, Munich (Germany); Dassinger, Benjamin [Medical University Innsbruck, Department of Neuroradiology, Innsbruck (Austria); Justus-Liebig-University Giessen, Department of Neuroradiology, Giessen (Germany); Forsting, Michael [University Hospital, University Duisburg-Essen, Departments of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Ladd, Mark E. [University Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); University Hospital, University Duisburg-Essen, Departments of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany)

    2014-03-15

    The purpose of this paper is to assess the value of 7 Tesla (7 T) MRI for the depiction of brain stem and cranial nerve (CN) anatomy. Six volunteers were examined at 7 T using high-resolution SWI, MPRAGE, MP2RAGE, 3D SPACE T2, T2, and PD images to establish scanning parameters targeted at optimizing spatial resolution. Direct comparisons between 3 and 7 T were performed in two additional subjects using the finalized sequences (3 T: T2, PD, MPRAGE, SWAN; 7 T: 3D T2, MPRAGE, SWI, MP2RAGE). Artifacts and the depiction of structures were evaluated by two neuroradiologists using a standardized score sheet. Sequences could be established for high-resolution 7 T imaging even in caudal cranial areas. High in-plane resolution T2, PD, and SWI images provided depiction of inner brain stem structures such as pons fibers, raphe, reticular formation, nerve roots, and periaqueductal gray. MPRAGE and MP2RAGE provided clear depiction of the CNs. 3D T2 images improved depiction of inner brain structure in comparison to T2 images at 3 T. Although the 7-T SWI sequence provided improved contrast to some inner structures, extended areas were influenced by artifacts due to image disturbances from susceptibility differences. Seven-tesla imaging of basal brain areas is feasible and might have significant impact on detection and diagnosis in patients with specific diseases, e.g., trigeminal pain related to affection of the nerve root. Some inner brain stem structures can be depicted at 3 T, but certain sequences at 7 T, in particular 3D SPACE T2, are superior in producing anatomical in vivo images of deep brain stem structures. (orig.)

  17. High-resolution anatomy of the human brain stem using 7-T MRI: improved detection of inner structures and nerves?

    International Nuclear Information System (INIS)

    Gizewski, Elke R.; Maderwald, Stefan; Linn, Jennifer; Bochmann, Katja; Dassinger, Benjamin; Forsting, Michael; Ladd, Mark E.

    2014-01-01

    The purpose of this paper is to assess the value of 7 Tesla (7 T) MRI for the depiction of brain stem and cranial nerve (CN) anatomy. Six volunteers were examined at 7 T using high-resolution SWI, MPRAGE, MP2RAGE, 3D SPACE T2, T2, and PD images to establish scanning parameters targeted at optimizing spatial resolution. Direct comparisons between 3 and 7 T were performed in two additional subjects using the finalized sequences (3 T: T2, PD, MPRAGE, SWAN; 7 T: 3D T2, MPRAGE, SWI, MP2RAGE). Artifacts and the depiction of structures were evaluated by two neuroradiologists using a standardized score sheet. Sequences could be established for high-resolution 7 T imaging even in caudal cranial areas. High in-plane resolution T2, PD, and SWI images provided depiction of inner brain stem structures such as pons fibers, raphe, reticular formation, nerve roots, and periaqueductal gray. MPRAGE and MP2RAGE provided clear depiction of the CNs. 3D T2 images improved depiction of inner brain structure in comparison to T2 images at 3 T. Although the 7-T SWI sequence provided improved contrast to some inner structures, extended areas were influenced by artifacts due to image disturbances from susceptibility differences. Seven-tesla imaging of basal brain areas is feasible and might have significant impact on detection and diagnosis in patients with specific diseases, e.g., trigeminal pain related to affection of the nerve root. Some inner brain stem structures can be depicted at 3 T, but certain sequences at 7 T, in particular 3D SPACE T2, are superior in producing anatomical in vivo images of deep brain stem structures. (orig.)

  18. Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants.

    Science.gov (United States)

    Shis, David L; Bennett, Matthew R

    2013-03-26

    The construction of synthetic gene circuits relies on our ability to engineer regulatory architectures that are orthogonal to the host's native regulatory pathways. However, as synthetic gene circuits become larger and more complicated, we are limited by the small number of parts, especially transcription factors, that work well in the context of the circuit. The current repertoire of transcription factors consists of a limited selection of activators and repressors, making the implementation of transcriptional logic a complicated and component-intensive process. To address this, we modified bacteriophage T7 RNA polymerase (T7 RNAP) to create a library of transcriptional AND gates for use in Escherichia coli by first splitting the protein and then mutating the DNA recognition domain of the C-terminal fragment to alter its promoter specificity. We first demonstrate that split T7 RNAP is active in vivo and compare it with full-length enzyme. We then create a library of mutant split T7 RNAPs that have a range of activities when used in combination with a complimentary set of altered T7-specific promoters. Finally, we assay the two-input function of both wild-type and mutant split T7 RNAPs and find that regulated expression of the N- and C-terminal fragments of the split T7 RNAPs creates AND logic in each case. This work demonstrates that mutant split T7 RNAP can be used as a transcriptional AND gate and introduces a unique library of components for use in synthetic gene circuits.

  19. Survival of Escherichia coli O157:H7 in Milk Exposed to High Temperatures and High Pressure**

    Directory of Open Access Journals (Sweden)

    Irena Usajewicz

    2006-01-01

    Full Text Available The objective of the present study was to determine the survival of two enterohemorrhagic Escherichia coli O157:H7 strains (no. 94 and 402 and a saprophytic E. coli 1 strain at temperatures of 55 and 60 °C, and under the pressure of 300 to 600 MPa at ambient temperature (about 20 °C. The strains, in populations of 106–107 CFU/mL, were introduced into the skim milk and broth. The survival of test strains at high temperatures and high pressure depended to a high degree (p<0.05 on the type of medium in which the cells were suspended. At 55 °C the inactivation of E. coli cells was recorded after 60 to 120 min in the broth, and after 180 min in the milk. At 60 °C the time required for their thermal death was 15 to 30 min in broth. In milk only E. coli 1 cells died after 30-minute heating; the other strains survived in populations of about 40 CFU/mL. In the broth, a pressure of 550 MPa, applied for 20 min at ambient temperature, killed the entire populations of E. coli 94 and E. coli 402, and all E. coli 1 cells died at 600 MPa, also applied for 20 min at ambient temperature. In the milk live cells of all pressurized strains survived in the quantities of 102–103 CFU/mL, so their reduction by 5 log cycles was not achieved. Damaged cells were found in the majority of samples exposed to heating and high pressure. These cells did not form colonies on nutrient agar, but were able to repair damage and grow in nutrient broth at 37 °C.

  20. Search for Enterohaemorrhagic Escherichia coli O157:H7 and ...

    African Journals Online (AJOL)

    Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 and Salmonella enterica are important zoonotic bacteria responsible for enteric infections in humans. The present study investigated the possible role of kittens in the zoonotic transmission of antimicrobial resistant EHEC O157 and Salmonella enterica to human using ...

  1. Accelerated high-resolution 3D magnetic resonance spectroscopic imaging in the brain At 7 T

    International Nuclear Information System (INIS)

    Hangel, G.

    2015-01-01

    With the announcement of the first series of magnetic resonance (MR) scanners with a field strength of 7 Tesla (T) intended for clinical practice, the development of high-performance sequences for higher field strengths has gained importance. Magnetic resonance spectroscopic imaging (MRSI) in the brain currently offers the unique ability to spatially resolve the distribution of multiple metabolites simultaneously. Its big diagnostic potential could be applied to many clinical protocols, for example the assessment of tumour treatment or progress of Multiple Sclerosis. Moving to ultra-high fields like 7 T has the main benefits of increased signal-to-noise ratio (SNR) and improved spectral quality, but brings its own challenges due to stronger field inhomogeneities. Necessary for a robust, flexible and useful MRSI sequence in the brain are high resolutions, shortened measurement times, the possibility for 3D-MRSI and the suppression of spectral contamination by trans-cranial lipids. This thesis addresses these limitations and proposes Hadamard spectroscopic imaging (HSI) as solution for multi-slice MRSI, the application of generalized autocalibrating partially parallel acquisition (GRAPPA) and spiral trajectories for measurement acceleration, non-selective inversion recovery (IR) lipid-suppression as well as combinations of these methods. Further, the optimisation of water suppression for 7 T systems and the acquisition of ultra-high resolution (UHR)-MRSI are discussed. In order to demonstrate the clinical feasibility of these approaches, MRSI measurement results of a glioma patient are presented. The discussion of the obtained results in the context of the state-of-art in 7 T MRSI in the brain, possible future applications as well as potential further improvements of the MRSI sequences conclude this thesis. (author) [de

  2. Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Common Strains of Escherichia coli▿

    Science.gov (United States)

    Hill, Joshua; Beriwal, Shilpa; Chandra, Ishwad; Paul, Vinod K.; Kapil, Aarti; Singh, Tripti; Wadowsky, Robert M.; Singh, Vinita; Goyal, Ankur; Jahnukainen, Timo; Johnson, James R.; Tarr, Phillip I.; Vats, Abhay

    2008-01-01

    We developed a highly sensitive and specific LAMP assay for Escherichia coli. It does not require DNA extraction and can detect as few as 10 copies. It detected all 36 of 36 E. coli isolates and all 22 urine samples (out of 89 samples tested) that had E. coli. This assay is rapid, low in cost, and simple to perform. PMID:18550738

  3. Loop-mediated isothermal amplification assay for rapid detection of common strains of Escherichia coli.

    Science.gov (United States)

    Hill, Joshua; Beriwal, Shilpa; Chandra, Ishwad; Paul, Vinod K; Kapil, Aarti; Singh, Tripti; Wadowsky, Robert M; Singh, Vinita; Goyal, Ankur; Jahnukainen, Timo; Johnson, James R; Tarr, Phillip I; Vats, Abhay

    2008-08-01

    We developed a highly sensitive and specific LAMP assay for Escherichia coli. It does not require DNA extraction and can detect as few as 10 copies. It detected all 36 of 36 E. coli isolates and all 22 urine samples (out of 89 samples tested) that had E. coli. This assay is rapid, low in cost, and simple to perform.

  4. Quadruplex MAPH: improvement of throughput in high-resolution copy number screening.

    Science.gov (United States)

    Tyson, Jess; Majerus, Tamsin Mo; Walker, Susan; Armour, John Al

    2009-09-28

    Copy number variation (CNV) in the human genome is recognised as a widespread and important source of human genetic variation. Now the challenge is to screen for these CNVs at high resolution in a reliable, accurate and cost-effective way. Multiplex Amplifiable Probe Hybridisation (MAPH) is a sensitive, high-resolution technology appropriate for screening for CNVs in a defined region, for a targeted population. We have developed MAPH to a highly multiplexed format ("QuadMAPH") that allows the user a four-fold increase in the number of loci tested simultaneously. We have used this method to analyse a genomic region of 210 kb, including the MSH2 gene and 120 kb of flanking DNA. We show that the QuadMAPH probes report copy number with equivalent accuracy to simplex MAPH, reliably demonstrating diploid copy number in control samples and accurately detecting deletions in Hereditary Non-Polyposis Colorectal Cancer (HNPCC) samples. QuadMAPH is an accurate, high-resolution method that allows targeted screening of large numbers of subjects without the expense of genome-wide approaches. Whilst we have applied this technique to a region of the human genome, it is equally applicable to the genomes of other organisms.

  5. Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.

    Science.gov (United States)

    Cowley, Lauren A; Beckett, Stephen J; Chase-Topping, Margo; Perry, Neil; Dallman, Tim J; Gally, David L; Jenkins, Claire

    2015-04-08

    Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age groups and disease severity. The aim of this study was to analyse the genome sequences of 16 (fourteen T4 and two T7) E. coli O157 typing phages and to determine the genes responsible for the subtle differences in phage type profiles. The typing phages were sequenced using paired-end Illumina sequencing at The Genome Analysis Centre and the Animal Health and Veterinary Laboratories Agency and bioinformatics programs including Velvet, Brig and Easyfig were used to analyse them. A two-way Euclidian cluster analysis highlighted the associations between groups of phage types and typing phages. The analysis showed that the T7 typing phages (9 and 10) differed by only three genes and that the T4 typing phages formed three distinct groups of similar genomic sequences: Group 1 (1, 8, 11, 12 and 15, 16), Group 2 (3, 6, 7 and 13) and Group 3 (2, 4, 5 and 14). The E. coli O157 phage typing scheme exhibited a significantly modular network linked to the genetic similarity of each group showing that these groups are specialised to infect a subset of phage types. Sequencing the typing phage has enabled us to identify the variable genes within each group and to determine how this corresponds to changes in phage type.

  6. Rapid and Accurate Detection of Bacteriophage Activity against Escherichia coli O157:H7 by Propidium Monoazide Real-Time PCR

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2014-01-01

    Full Text Available Conventional methods to determine the efficacy of bacteriophage (phage for biocontrol of E. coli require several days, due to the need to culture bacteria. Furthermore, cell surface-attached phage particles may lyse bacterial cells during experiments, leading to an overestimation of phage activity. DNA-based real-time quantitative polymerase chain reaction (qPCR is a fast, sensitive, and highly specific means of enumerating pathogens. However, qPCR may underestimate phage activity due to its inability to distinguish viable from nonviable cells. In this study, we evaluated the suitability of propidium monoazide (PMA, a microbial membrane-impermeable dye that inhibits amplification of extracellular DNA and DNA within dead or membrane-compromised cells as a means of using qPCR to identify only intact E. coli cells that survive phage exposure. Escherichia coli O157:H7 strain R508N and 4 phages (T5-like, T1-like, T4-like, and O1-like were studied. Results compared PMA-qPCR and direct plating and confirmed that PMA could successfully inhibit amplification of DNA from compromised/damaged cells E. coli O157:H7. Compared to PMA-qPCR, direct plating overestimated (P < 0.01 phage efficacy as cell surface-attached phage particles lysed E. coli O157:H7 during the plating process. Treatment of samples with PMA in combination with qPCR can therefore be considered beneficial when assessing the efficacy of bacteriophage for biocontrol of E. coli O157:H7.

  7. Decomposing highly edge-connected graphs into homomorphic copies of a fixed tree

    DEFF Research Database (Denmark)

    Merker, Martin

    2016-01-01

    far this conjecture has only been verified for paths, stars, and a family of bistars. We prove a weaker version of the Tree Decomposition Conjecture, where we require the subgraphs in the decomposition to be isomorphic to graphs that can be obtained from T by vertex-identifications. We call......The Tree Decomposition Conjecture by Barát and Thomassen states that for every tree T there exists a natural number k(T) such that the following holds: If G is a k(T)-edge-connected simple graph with size divisible by the size of T, then G can be edge-decomposed into subgraphs isomorphic to T. So...... such a subgraph a homomorphic copy of T. This implies the Tree Decomposition Conjecture under the additional constraint that the girth of G is greater than the diameter of T. As an application, we verify the Tree Decomposition Conjecture for all trees of diameter at most 4....

  8. Characterization of a ViI-like Phage Specific to Escherichia coli O157:H7

    Directory of Open Access Journals (Sweden)

    Kropinski Andrew M

    2011-09-01

    Full Text Available Abstract Phage vB_EcoM_CBA120 (CBA120, isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra.

  9. 4 CFR 22.7 - Copies and Service Thereof [Rule 7].

    Science.gov (United States)

    2010-01-01

    ...)], shall be provided to the Board by e-mail at [email protected], with a courtesy copy of the submission provided... delivery, express or priority mail, or approved commercial carrier (e.g., UPS or FedEx) within 2 business...

  10. Revealing localization and regulation of GTPase PmRab7 in lymphoid cells of Penaeus monodon after WSSV infection

    Directory of Open Access Journals (Sweden)

    Amrendra Kumar

    2016-10-01

    Full Text Available Objective: To identify white spot syndrome virus (WSSV entry into the host-cells of the cultured shrimp Penaeus monodon, we have attempted to localize PmRab7 (Ras-related in brain which is playing a vital role in the WSSV internalization. Methods: In this study, we have cloned PmRab7 and expressed in Escherichia coli, further purified rPmRab7 was used for antibody production, isolation of lysosomal sub-cellular fractions and western blot against lysosomal protein. Moreover, high fold-change in PmRab7 regulation with increasing copy number of WSSV has been studied by using real-time PCR. Results: 651 bp amplicon size gene was successfully amplified, ligated amplicon with pTZ T-tail vector confirmed by colony PCR and retriction enzyme digestion on agarose gel. Subcloned (pRSET-B 651 bp gene transformed successfully in Rosetta and after 6 h of induction expressed rPmRab7 was on SDS page, furthermore soluble fraction of rPmRab7 (26 kDa was purified by ni-NTA column. AntiPmRab7 antibody was received by Merk Pvt. Ltd., and western blot analysis revealed that PmRab7 is present in the lysosomal sub-cellular fraction. Copy number of WSSV was increased 5 fold in 24 h and 20 fold in 72 h of infection and subsequently transcrtipt of PmRab7 was Ct = 1.0 to Ct = 8.5. Conclusions: Presence of PmRab7 on lysosome clearly indicating PmRab7 participating in lysosomal maturation, other hand WSSV may follow the same route of entry. WSSV internalization has directly linked with regulation of PmRab7.

  11. The Escherichia coli antiterminator protein BglG stabilizes the 5 ...

    Indian Academy of Sciences (India)

    Unknown

    Keywords. Antitermination; mRNA stability; RNA binding protein ... factor, Rho, and the pBR322 copy number protein, Rop, have been .... Transcription analysis using the oligo- ..... Retarded RNA turnover in Escherichia coli a means of main-.

  12. Quadruplex MAPH: improvement of throughput in high-resolution copy number screening

    Directory of Open Access Journals (Sweden)

    Walker Susan

    2009-09-01

    Full Text Available Abstract Background Copy number variation (CNV in the human genome is recognised as a widespread and important source of human genetic variation. Now the challenge is to screen for these CNVs at high resolution in a reliable, accurate and cost-effective way. Results Multiplex Amplifiable Probe Hybridisation (MAPH is a sensitive, high-resolution technology appropriate for screening for CNVs in a defined region, for a targeted population. We have developed MAPH to a highly multiplexed format ("QuadMAPH" that allows the user a four-fold increase in the number of loci tested simultaneously. We have used this method to analyse a genomic region of 210 kb, including the MSH2 gene and 120 kb of flanking DNA. We show that the QuadMAPH probes report copy number with equivalent accuracy to simplex MAPH, reliably demonstrating diploid copy number in control samples and accurately detecting deletions in Hereditary Non-Polyposis Colorectal Cancer (HNPCC samples. Conclusion QuadMAPH is an accurate, high-resolution method that allows targeted screening of large numbers of subjects without the expense of genome-wide approaches. Whilst we have applied this technique to a region of the human genome, it is equally applicable to the genomes of other organisms.

  13. Phosphorolytic activity of Escherichia coli glycyl-tRNA synthetase towards its cognate aminoacyl adenylate detected by 31P-NMR spectroscopy and thin-layer chromatography

    DEFF Research Database (Denmark)

    Led, Jens Jørgen; Switon, Werner K.; Jensen, Kaj Frank

    1983-01-01

    The catalytic activity of highly purified Escherichia coli glycyl-tRNA synthetase has been studied by 31P-NMR spectroscopy and thin-layer chromatography on poly(ethyleneimine)-cellulose. It was found that this synthetase, besides the activation of its cognate amino acid and the syntheses...

  14. Differential gene expression by integrin β7+ and β7- memory T helper cells

    Directory of Open Access Journals (Sweden)

    Yang Yee

    2004-07-01

    Full Text Available Abstract Background The cell adhesion molecule integrin α4β7 helps direct the migration of blood lymphocytes to the intestine and associated lymphoid tissues. We hypothesized that β7+ and β7- blood memory T helper cells differ in their expression of genes that play a role in the adhesion or migration of T cells. Results RNA was prepared from β7+ and β7- CD4+ CD45RA- blood T cells from nine normal human subjects and analyzed using oligonucleotide microarrays. Of 21357 genes represented on the arrays, 16 were more highly expressed in β7+ cells and 18 were more highly expressed in β7- cells (≥1.5 fold difference and adjusted P + memory/effector T cells than on β7- cells. Conclusions Memory/effector T cells that express integrin β7 have a distinct pattern of expression of a set of gene transcripts. Several of these molecules can affect cell adhesion or chemotaxis and are therefore likely to modulate the complex multistep process that regulates trafficking of CD4+ memory T cell subsets with different homing behaviors.

  15. Potential application of high hydrostatic pressure to eliminate Escherichia coli O157:H7 on alfalfa sprouted seeds.

    Science.gov (United States)

    Neetoo, Hudaa; Ye, Mu; Chen, Haiqiang

    2008-12-10

    Sprouts eaten raw are increasingly being perceived as hazardous foods as they have been implicated in Escherichia coli O157:H7 outbreaks where the seeds were found to be the likely source of contamination. The objective of our study was to evaluate the potential of using high hydrostatic pressure (HHP) technology for alfalfa seed decontamination. Alfalfa seeds inoculated with a cocktail of five strains of E. coli O157:H7 were subjected to pressures of 500 and 600 MPa for 2 min at 20 degrees C in a dry or wet (immersed in water) state. Immersing seeds in water during pressurization considerably enhanced inactivation of E. coli O157:H7 achieving reductions of 3.5 log and 5.7 log at 500 and 600 MPa, respectively. When dry seeds were pressurized, both pressure levels reduced the counts by 5 log reduction in the population was achieved when 600 MPa was applied for durations of > or =6 min although survivors were still detected by enrichment. When the pressure was stepped up to 650 MPa, the threshold time required to achieve complete elimination was 15 min. Un-inoculated seeds pressure-treated at 650 MPa for 15 min at 20 degrees C successfully sprouted achieving a germination rate identical to untreated seeds after eight days of sprouting. These results therefore demonstrate the promising application of HHP on alfalfa seeds to eliminate the risk of E. coli O157:H7 infections associated with consumption of raw alfalfa sprouts.

  16. Isolation of Campylobacter spp and Escherichia coli 0157: H7 from ...

    African Journals Online (AJOL)

    Objectives: To determine the biosafety of a free range indigenous chicken value chain with reference to zoonotic bacteria, Campylobacter spp and Escherichia coli 0157: H7. Design: cross-sectional sampling of chickens and chicken meat carcasses at farm and market level. Setting: Makueni and Nairobi Counties. Subjects: ...

  17. High-resolution functional MRI of the human amygdala at 7 T

    Energy Technology Data Exchange (ETDEWEB)

    Sladky, Ronald, E-mail: ronald.sladky@meduniwien.ac.at [MR Centre of Excellence, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna (Austria); Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna (Austria); Baldinger, Pia; Kranz, Georg S. [Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna (Austria); Tröstl, Jasmin [MR Centre of Excellence, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna (Austria); Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna (Austria); Höflich, Anna; Lanzenberger, Rupert [Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna (Austria); Moser, Ewald [MR Centre of Excellence, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna (Austria); Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna (Austria); Windischberger, Christian, E-mail: christian.windischberger@meduniwien.ac.at [MR Centre of Excellence, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna (Austria); Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna (Austria)

    2013-05-15

    Functional magnetic resonance imaging (fMRI) has become the primary non-invasive method for investigating the human brain function. With an increasing number of ultra-high field MR systems worldwide possibilities of higher spatial and temporal resolution in combination with increased sensitivity and specificity are expected to advance detailed imaging of distinct cortical brain areas and subcortical structures. One target region of particular importance to applications in psychiatry and psychology is the amygdala. However, ultra-high field magnetic resonance imaging of these ventral brain regions is a challenging endeavor that requires particular methodological considerations. Ventral brain areas are particularly prone to signal losses arising from strong magnetic field inhomogeneities along susceptibility borders. In addition, physiological artifacts from respiration and cardiac action cause considerable fluctuations in the MR signal. Here we show that, despite these challenges, fMRI data from the amygdala may be obtained with high temporal and spatial resolution combined with increased signal-to-noise ratio. Maps of neural activation during a facial emotion discrimination paradigm at 7 T are presented and clearly show the gain in percental signal change compared to 3 T results, demonstrating the potential benefits of ultra-high field functional MR imaging also in ventral brain areas.

  18. High-resolution functional MRI of the human amygdala at 7 T

    International Nuclear Information System (INIS)

    Sladky, Ronald; Baldinger, Pia; Kranz, Georg S.; Tröstl, Jasmin; Höflich, Anna; Lanzenberger, Rupert; Moser, Ewald; Windischberger, Christian

    2013-01-01

    Functional magnetic resonance imaging (fMRI) has become the primary non-invasive method for investigating the human brain function. With an increasing number of ultra-high field MR systems worldwide possibilities of higher spatial and temporal resolution in combination with increased sensitivity and specificity are expected to advance detailed imaging of distinct cortical brain areas and subcortical structures. One target region of particular importance to applications in psychiatry and psychology is the amygdala. However, ultra-high field magnetic resonance imaging of these ventral brain regions is a challenging endeavor that requires particular methodological considerations. Ventral brain areas are particularly prone to signal losses arising from strong magnetic field inhomogeneities along susceptibility borders. In addition, physiological artifacts from respiration and cardiac action cause considerable fluctuations in the MR signal. Here we show that, despite these challenges, fMRI data from the amygdala may be obtained with high temporal and spatial resolution combined with increased signal-to-noise ratio. Maps of neural activation during a facial emotion discrimination paradigm at 7 T are presented and clearly show the gain in percental signal change compared to 3 T results, demonstrating the potential benefits of ultra-high field functional MR imaging also in ventral brain areas

  19. High Frequency of Copy-Neutral Loss of Heterozygosity in Patients with Myelofibrosis.

    Science.gov (United States)

    Rego de Paula Junior, Milton; Nonino, Alexandre; Minuncio Nascimento, Juliana; Bonadio, Raphael S; Pic-Taylor, Aline; de Oliveira, Silviene F; Wellerson Pereira, Rinaldo; do Couto Mascarenhas, Cintia; Forte Mazzeu, Juliana

    2018-01-01

    Myelofibrosis is the rarest and most severe type of Philadelphia-negative classical myeloproliferative neoplasms. Although mutually exclusive driver mutations in JAK2, MPL, or CALR that activate JAK-STAT pathway have been related to the pathogenesis of the disease, chromosome abnormalities have also been associated with the phenotype and prognosis of the disease. Here, we report the use of a chromosomal microarray platform consisting of both oligo and SNP probes to improve the detection of chromosome abnormalities in patients with myelofibrosis. Sixteen patients with myelofibrosis were tested, and the results were compared to karyotype analysis. Driver mutations in JAK2, MPL, or CALR were investigated by PCR and MLPA. Conventional cytogenetics revealed chromosome abnormalities in 3 out of 16 cases (18.7%), while chromosomal microarray analysis detected copy-number variations (CNV) or copy-neutral loss of heterozygosity (CN-LOH) alterations in 11 out of 16 (68.7%) patients. These included 43 CN-LOH, 14 deletions, 1 trisomy, and 1 duplication. Ten patients showed multiple chromosomal abnormalities, varying from 2 to 13 CNVs or CN-LOHs. Mutational status for JAK2, CALR, and MPL by MLPA revealed a total of 3/16 (18.7%) patients positive for the JAK2 V617F mutation, 9 with CALR deletion or insertion and 1 positive for MPL mutation. Considering that most of the CNVs identified were smaller than the karyotype resolution and the high frequency of CN-LOHs in our study, we propose that chromosomal microarray platforms that combine oligos and SNP should be used as a first-tier genetic test in patients with myelofibrosis. © 2018 S. Karger AG, Basel.

  20. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

    Science.gov (United States)

    Armour, John A L; Palla, Raquel; Zeeuwen, Patrick L J M; den Heijer, Martin; Schalkwijk, Joost; Hollox, Edward J

    2007-01-01

    Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies.

  1. Detection and quantification of proviral HIV-1 184 M/V in circulating CD4(+) T cells of patients on HAART with a viremia less than 1000 copies/ml

    DEFF Research Database (Denmark)

    Mohey, Rajesh; Jørgensen, Anne Louise; Møller, Bjarne K

    2005-01-01

    and incorporation of resistant forms in the long-lived CD4+ T cellular DNA compartment is not clear. Objective To investigate the relationship between lamivudine associated mutant-type 184V and the wild-type 184M proviral forms in the circulating CD4+ T cells of patients and low-level viremia. Study design Cross-sectional......Background Highly active anti-retroviral therapy (HAART) effectively reduces HIV replication but does not completely hinder it. Sub-optimal therapy leads to HIV resistance to the drugs administered. However, the role of low-level viremia (viral-load less than 1000 copies/ml) on mutation genesis...... study of 50 patients on long-term HAART, with a viremia of less than 1000 copies/ml. Patients were stratified into three groups; on lamivudine, group I (viral load

  2. Comparison of 7T and 3T MRI in patients with moyamoya disease.

    Science.gov (United States)

    Oh, Byeong Ho; Moon, Hyeong Cheol; Baek, Hyeon Man; Lee, Youn Joo; Kim, Sang Woo; Jeon, Young Jai; Lee, Gun Seok; Kim, Hong Rae; Choi, Jai Ho; Min, Kyung Soo; Lee, Mou Seop; Kim, Young Gyu; Kim, Dong Ho; Kim, Won Seop; Park, Young Seok

    2017-04-01

    Magnetic resonance imaging and magnetic resonance angiography (MRI/MRA) are widely used for evaluating the moyamoya disease (MMD). This study compared the diagnostic accuracy of 7Tesla (T) and 3T MRI/MRA in MMD. In this case control study, 12 patients [median age: 34years; range (10-66years)] with MMD and 12 healthy controls [median age: 25years; range (22-59years)] underwent both 7T and 3T MRI/MRA. To evaluate the accuracy of MRI/MRA in MMD, five criteria were compared between imaging systems of 7T and 3T: Suzuki grading system, internal carotid artery (ICA) diameter, ivy sign, flow void of the basal ganglia on T2-weighted images, and high signal intensity areas of the basal ganglia on time-of-flight (TOF) source images. No difference was observed between 7T and 3T MRI/MRA in Suzuki stage, ICA diameter, and ivy sign score; while, 7T MRI/MRA showed a higher detection rate in the flow void on T2-weighted images and TOF source images (p<0.001). Receiver operating characteristic curves of both T2 and TOF criteria showed that 7T MRI/MRA had higher sensitivity and specificity than 3T MRI/MRA. Our findings indicate that 7T MRI/MRA is superior to 3T MRI/MRA for the diagnosis of MMD in point of detecting the flow void in basal ganglia by T2-weighted and TOF images. Copyright © 2016. Published by Elsevier Inc.

  3. A rapid and highly sensitive protocol for the detection of Escherichia coli O157:H7 based on immunochromatography assay combined with the enrichment technique of immunomagnetic nanoparticles

    Directory of Open Access Journals (Sweden)

    Qi H

    2011-11-01

    Full Text Available Hui Qi1, Zhen Zhong1, Han-Xin Zhou1, Chun-Yan Deng1, Hai Zhu2, Jin-Feng Li2, Xi-Li Wang2, Fu-Rong Li1,31Clinical Medical Research Center, The Second Clinical Medical College (Shenzhen People's Hospital, Jinan University, 2Shenzhen Bioeasy Biotechnologies Co, Ltd, 3Shenzhen Institute of Gerontology, Shenzhen, People's Republic of ChinaBackground: Escherichia coli O157:H7 (E. coli O157:H7 is an important pathogenic bacterium that threatens human health. A rapid, simple, highly sensitive, and specific method for the detection of E. coli O157:H7 is necessary.Methods: In the present study, immunomagnetic nanoparticles (IMPs were prepared with nanopure iron as the core, coated with E. coli O157:H7 polyclonal antibodies. These IMPs were used in combination with immunochromatographic assay (ICA and used to establish highly sensitive and rapid kits (IMPs+ICA to detect E. coli O157:H7. The kits were then used to detect E. coli O157:H7 in 150 food samples and were compared with conventional ICA to evaluate their efficacy.Results: The average diameter of IMPs was 56 nm and the amount of adsorbed antibodies was 106.0 µg/mg. The sensitivity of ICA and IMPs+ICA was 105 colony-forming units/mL and 103 CFUs/mL, respectively, for purified E. coli O157:H7 solution. The sensitivity of IMPs+ICA was increased by two orders, and its specificity was similar to ICA.Conclusion: The kits have the potential to offer important social and economic benefits in the screening, monitoring, and control of food safety.Keywords: colloidal gold, immunomagnetic nanoparticles, Escherichia coli O157:H7, immunochromatographic assay

  4. Distribution of espM and espT among enteropathogenic and enterohaemorrhagic Escherichia coli

    Science.gov (United States)

    Arbeloa, Ana; Blanco, Miguel; Moreira, Fabiana C.; Bulgin, Richard; López, Cecilia; Dahbi, Ghizlane; Blanco, Jesús E.; Mora, Azucena; Alonso, María Pilar; Mamani, Rosalia Ceferina; Gomes, Tânia A. T.; Blanco, Jorge; Frankel, Gad

    2009-01-01

    Enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) translocate dozens of type III secretion system effectors, including the WxxxE effectors Map, EspM and EspT that activate Rho GTPases. While map, which is carried on the LEE pathogenicity island, is absolutely conserved among EPEC and EHEC strains, the prevalence of espM and espT is not known. Here we report the results of a large screen aimed at determining the prevalence of espM and espT among clinical EPEC and EHEC isolates. The results suggest that espM, detected in 51 % of the tested strains, is more commonly found in EPEC and EHEC serogroups that are linked to severe human infections. In contrast, espT was absent from all the EHEC isolates and was found in only 1.8 % of the tested EPEC strains. Further characterization of the virulence gene repertoire of the espT-positive strains led to the identification of a new ζ2 intimin variant. All the espT-positive strains but two contained the tccP gene. espT was first found in Citrobacter rodentium and later in silico in EPEC E110019, which is of particular interest as this strain was responsible for a particularly severe diarrhoeal outbreak in Finland in 1987 that affected 650 individuals in a school complex and an additional 137 associated household members. Comparing the protein sequences of EspT to that of E110019 showed a high level of conservation, with only three strains encoding EspT that differed in 6 amino acids. At present, it is not clear why espT is so rare, and what impact EspM and EspT have on EPEC and EHEC infection. PMID:19528152

  5. Development of a dual vaccine for prevention of Brucella abortus infection and Escherichia coli O157:H7 intestinal colonization.

    Science.gov (United States)

    Iannino, Florencia; Herrmann, Claudia K; Roset, Mara S; Briones, Gabriel

    2015-05-05

    Zoonoses that affect human and animal health have an important economic impact. In the study now presented, a bivalent vaccine has been developed that has the potential for preventing the transmission from cattle to humans of two bacterial pathogens: Brucella abortus and Shiga toxin-producing Escherichia coli (STEC). A 66kDa chimeric antigen, composed by EspA, Intimin, Tir, and H7 flagellin (EITH7) from STEC, was constructed and expressed in B. abortus Δpgm vaccine strain (BabΔpgm). Mice orally immunized with BabΔpgm(EITH7) elicited an immune response with the induction of anti-EITH7 antibodies (IgA) that clears an intestinal infection of E. coli O157:H7 three times faster (t=4 days) than mice immunized with BabΔpgm carrier strain (t=12 days). As expected, mice immunized with BabΔpgm(EITH7) strain also elicited a protective immune response against B. abortus infection. A Brucella-based vaccine platform is described capable of eliciting a combined protective immune response against two bacterial pathogens with diverse lifestyles-the intracellular pathogen B. abortus and the intestinal extracellular pathogen STEC. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Pediatric-specific\tAntimicrobial\tResistance\tPatterns\tof\tUrinary\tTract\tInfections: A\tSingle-Centre\tExperience\tfrom\tTurkey

    Directory of Open Access Journals (Sweden)

    Yasar Kandur

    2016-12-01

    Full Text Available Objectives: Antimicrobial resistance of the causative microorganisms of pediatric urinary tract infection (UTI is a growing problem.\tThe\taim\tof\tthis\tstudy\tis\tto\tdetermine\tthe\tchanging\tpattern\tof\tantibiotic\tsusceptibility\tin\tUTIs\tin\tan\toutpatient\tsetting. Methods: We\tretrospectively\treviewed\tthe\tmedical\trecords\tof\tpediatric\tpatients\twith\tUTI\twho\twere\tfollowed-up\tin\tour\tcenter between\tJanuary-2014\tand\tMay-2015. Results: One hundred and seventy-one patients (M/F= 53/118;\tmean age 56 ± 47.2\tmonths with UTI were enrolled\tin this study.\tA\ttotal\tof\t231\turinary\tpathogens\twere\tisolated\tfrom\tUTI\tepisodes.\tThe\tmost\tcommon\tcausative\tagent\twas\tEscherichia\tcoli (E. coli (70.6% followed by Klebsiella spp. (16.5%, Proteus spp. (6.5%. One point eight percent of E. coli isolates were resistant to amikacin, 17.8% to gentamicin, 60.7% to TMP-SMX, 66,9% to ampicillin, 52.1% to cefixime, 46% to ceftriaxone, 54.6%\tto\tcefuroxime\tand\t4.9%\tto\tnitrofurantoin. Conclusions: TMP-SMX and nitrofurantoin are poor empirical choices for pediatric patients due high resistance rates and gastrointestinal side effects, respectively. Second and third -generation cephalosporins (cefixime may not be considered as appropriate\tempiric\tantibiotic\talternatives\tanymore\tgiven\ttheir\thigh\tresistance\trates\tin\tthe\tnext\tfew\tyears.\tPhysicians\twho\twork in\tthe\tprimary\thealth\tcare\tshould\tbe\tencouraged\tfor\tthe\tselection\tof\tmore\tappropriate\tantibiotics.

  7. Blockade of CD7 expression in T cells for effective chimeric antigen receptor targeting of T-cell malignancies.

    Science.gov (United States)

    Png, Yi Tian; Vinanica, Natasha; Kamiya, Takahiro; Shimasaki, Noriko; Coustan-Smith, Elaine; Campana, Dario

    2017-11-28

    Effective immunotherapies for T-cell malignancies are lacking. We devised a novel approach based on chimeric antigen receptor (CAR)-redirected T lymphocytes. We selected CD7 as a target because of its consistent expression in T-cell acute lymphoblastic leukemia (T-ALL), including the most aggressive subtype, early T-cell precursor (ETP)-ALL. In 49 diagnostic T-ALL samples (including 14 ETP-ALL samples), median CD7 expression was >99%; CD7 expression remained high at relapse (n = 14), and during chemotherapy (n = 54). We targeted CD7 with a second-generation CAR (anti-CD7-41BB-CD3ζ), but CAR expression in T lymphocytes caused fratricide due to the presence of CD7 in the T cells themselves. To downregulate CD7 and control fratricide, we applied a new method (protein expression blocker [PEBL]), based on an anti-CD7 single-chain variable fragment coupled with an intracellular retention domain. Transduction of anti-CD7 PEBL resulted in virtually instantaneous abrogation of surface CD7 expression in all transduced T cells; 2.0% ± 1.7% were CD7 + vs 98.1% ± 1.5% of mock-transduced T cells (n = 5; P < .0001). PEBL expression did not impair T-cell proliferation, interferon-γ and tumor necrosis factor-α secretion, or cytotoxicity, and eliminated CAR-mediated fratricide. PEBL-CAR T cells were highly cytotoxic against CD7 + leukemic cells in vitro and were consistently more potent than CD7 + T cells spared by fratricide. They also showed strong anti-leukemic activity in cell line- and patient-derived T-ALL xenografts. The strategy described in this study fits well with existing clinical-grade cell manufacturing processes and can be rapidly implemented for the treatment of patients with high-risk T-cell malignancies.

  8. Mapping Escherichia coli elongation factor Tu residues involved in binding of aminoacyl-tRNA

    DEFF Research Database (Denmark)

    Wiborg, Ove; Andersen, C; Knudsen, Charlotte Rohde

    1996-01-01

    Two residues of Escherichia coli elongation factor Tu involved in binding of aminoacyl-tRNA were identified and subjected to mutational analysis. Lys-89 and Asn-90 were each replaced by either Ala or Glu. The four single mutants were denoted K89A, K89E, N90A, and N90E, respectively. The mutants...... were characterized with respect to thermal and chemical stability, GTPase activity, tRNA affinity, and activity in an in vitro translation assay. Most conspicuously tRNA affinities were reduced for all mutants. The results verify our structural analysis of elongation factor Tu in complex with aminoacyl....... Their functional roles are discussed in relation to the structure of elongation factor Tu in complex with aminoacyl-tRNA. Udgivelsesdato: 1996-Aug-23...

  9. Analysis of T-DNA/Host-Plant DNA Junction Sequences in Single-Copy Transgenic Barley Lines

    Directory of Open Access Journals (Sweden)

    Joanne G. Bartlett

    2014-01-01

    Full Text Available Sequencing across the junction between an integrated transfer DNA (T-DNA and a host plant genome provides two important pieces of information. The junctions themselves provide information regarding the proportion of T-DNA which has integrated into the host plant genome, whilst the transgene flanking sequences can be used to study the local genetic environment of the integrated transgene. In addition, this information is important in the safety assessment of GM crops and essential for GM traceability. In this study, a detailed analysis was carried out on the right-border T-DNA junction sequences of single-copy independent transgenic barley lines. T-DNA truncations at the right-border were found to be relatively common and affected 33.3% of the lines. In addition, 14.3% of lines had rearranged construct sequence after the right border break-point. An in depth analysis of the host-plant flanking sequences revealed that a significant proportion of the T-DNAs integrated into or close to known repetitive elements. However, this integration into repetitive DNA did not have a negative effect on transgene expression.

  10. Comparison of 3 T and 7 T MRI clinical sequences for ankle imaging

    Energy Technology Data Exchange (ETDEWEB)

    Juras, Vladimir, E-mail: vladimir.juras@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Slovak Academy of Sciences, Institute of Measurement Science, Dubravska cesta 9, 84104 Bratislava (Slovakia); Welsch, Goetz, E-mail: welsch@bwh.harvard.edu [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Baer, Peter, E-mail: baerpeter@siemens.com [Siemens Healthcare, Richard-Strauss-Strasse 76, D81679 Munich (Germany); Kronnerwetter, Claudia, E-mail: claudia.kronnerwetter@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Fujita, Hiroyuki, E-mail: hiroyuki.fujita@qualedyn.com [Quality Electrodynamics, LCC, 777 Beta Dr, Cleveland, OH 44143-2336 (United States); Trattnig, Siegfried, E-mail: siegfried.trattnig@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria)

    2012-08-15

    The purpose of this study was to compare 3 T and 7 T signal-to-noise and contrast-to noise ratios of clinical sequences for imaging of the ankles with optimized sequences and dedicated coils. Ten healthy volunteers were examined consecutively on both systems with three clinical sequences: (1) 3D gradient-echo, T{sub 1}-weighted; (2) 2D fast spin-echo, PD-weighted; and (3) 2D spin-echo, T{sub 1}-weighted. SNR was calculated for six regions: cartilage; bone; muscle; synovial fluid; Achilles tendon; and Kager's fat-pad. CNR was obtained for cartilage/bone, cartilage/fluid, cartilage/muscle, and muscle/fat-pad, and compared by a one-way ANOVA test for repeated measures. Mean SNR significantly increased at 7 T compared to 3 T for 3D GRE, and 2D TSE was 60.9% and 86.7%, respectively. In contrast, an average SNR decrease of almost 25% was observed in the 2D SE sequence. A CNR increase was observed in 2D TSE images, and in most 3D GRE images. There was a substantial benefit from ultra high-field MR imaging of ankles with routine clinical sequences at 7 T compared to 3 T. Higher SNR and CNR at ultra-high field MR scanners may be useful in clinical practice for ankle imaging. However, carefully optimized protocols and dedicated extremity coils are necessary to obtain optimal results.

  11. Irradiation effect of escherichia coli O157 : H7 in meats

    International Nuclear Information System (INIS)

    Ito, Hitoshi; Harsojo

    1998-01-01

    Escherichia coli O157 : H7 is a rapidly emerging food-born pathogen which has been linked to outbreaks of hemorrhagic diarrhea in Japan, USA or many European countries. From this study, two strains of E. coli O157 : H7 were isolated from beef and chicken meats in each one sample of 4 replicates. Some of the biochemical characteristics of these isolates were different from type strain IID959. These isolates could grow quickly at 10degC on cultivation of nutrient agar. D 10 value of these isolates were obtained to be 0.06kGy in 0.067M phosphate buffer suspension which were highly sensitive than D 10 value of 0.12kGy on type strain IID959. On the irradiation effect of type strain IID959 in ground beef, D 10 value was obtained as 0.26kGy at fresh condition and 0.46kGy at frozen condition, respectively. From these results, necessary dose for elimination of E. coli O157 : H7 was decided as 1.5kGy for fresh meats and 3kGy for frozen meats. (author)

  12. Chromosomal replication incompatibility in Dam methyltransferase deficient Escherichia coli cells

    DEFF Research Database (Denmark)

    Freiesleben, Ulrik Von

    1996-01-01

    Dam methyltransferase deficient Escherichia coli cells containing minichromosomes were constructed. Free plasmid DNA could not be detected in these cells and the minichromosomes were found to be integrated in multiple copies in the origin of replication (oriC) region of the host chromosome....... The absence of the initiation cascade in Dam- cells is proposed to account for this observation of apparent incompatibility between plasmid and chromosomal copies of oriC. Studies using oriC-pBR322 chimeric plasmids and their deletion derivatives indicated that the incompatibility determinant is an intact...

  13. Engineered promoters enable constant gene expression at any copy number in bacteria.

    Science.gov (United States)

    Segall-Shapiro, Thomas H; Sontag, Eduardo D; Voigt, Christopher A

    2018-04-01

    The internal environment of growing cells is variable and dynamic, making it difficult to introduce reliable parts, such as promoters, for genetic engineering. Here, we applied control-theoretic ideas to design promoters that maintained constant levels of expression at any copy number. Theory predicts that independence to copy number can be achieved by using an incoherent feedforward loop (iFFL) if the negative regulation is perfectly non-cooperative. We engineered iFFLs into Escherichia coli promoters using transcription-activator-like effectors (TALEs). These promoters had near-identical expression in different genome locations and plasmids, even when their copy number was perturbed by genomic mutations or changes in growth medium composition. We applied the stabilized promoters to show that a three-gene metabolic pathway to produce deoxychromoviridans could retain function without re-tuning when the stabilized-promoter-driven genes were moved from a plasmid into the genome.

  14. MRI of the hip at 7T: feasibility of bone microarchitecture, high-resolution cartilage, and clinical imaging.

    Science.gov (United States)

    Chang, Gregory; Deniz, Cem M; Honig, Stephen; Egol, Kenneth; Regatte, Ravinder R; Zhu, Yudong; Sodickson, Daniel K; Brown, Ryan

    2014-06-01

    To demonstrate the feasibility of performing bone microarchitecture, high-resolution cartilage, and clinical imaging of the hip at 7T. This study had Institutional Review Board approval. Using an 8-channel coil constructed in-house, we imaged the hips of 15 subjects on a 7T magnetic resonance imaging (MRI) scanner. We applied: 1) a T1-weighted 3D fast low angle shot (3D FLASH) sequence (0.23 × 0.23 × 1-1.5 mm(3) ) for bone microarchitecture imaging; 2) T1-weighted 3D FLASH (water excitation) and volumetric interpolated breath-hold examination (VIBE) sequences (0.23 × 0.23 × 1.5 mm(3) ) with saturation or inversion recovery-based fat suppression for cartilage imaging; 3) 2D intermediate-weighted fast spin-echo (FSE) sequences without and with fat saturation (0.27 × 0.27 × 2 mm) for clinical imaging. Bone microarchitecture images allowed visualization of individual trabeculae within the proximal femur. Cartilage was well visualized and fat was well suppressed on FLASH and VIBE sequences. FSE sequences allowed visualization of cartilage, the labrum (including cartilage and labral pathology), joint capsule, and tendons. This is the first study to demonstrate the feasibility of performing a clinically comprehensive hip MRI protocol at 7T, including high-resolution imaging of bone microarchitecture and cartilage, as well as clinical imaging. Copyright © 2013 Wiley Periodicals, Inc.

  15. Screening for virulence genes in Escherichia coli O157:H7 obtained ...

    African Journals Online (AJOL)

    Eighty (80) sources of drinking water comprising boreholes (24), streams (3), wells (29), pipe-borne (5) and 19 sachet water samples were collected between March 2014 and February 2015. Escherichia coli (E.coli) O157:H7 was isolated by enrichment in Tryptone soy broth at elevated temperature and streaking on Eosin ...

  16. Effect of heat treatment on the survival of Escherichia Coli O157:H7 ...

    African Journals Online (AJOL)

    The survival of Escherichia coli O157:H7 in raw milk treated in experimental pasteurizer was investigated in the year 2010. Raw milk was inoculated with different initial concentrations of E. coli O157:H7 and heated for 15 seconds at temperatures ranging from 69OC to 73OC. E. coli O157:H7 cells were not isolated from the ...

  17. Association between the SMN2 gene copy number and clinical characteristics of patients with spinal muscular atrophy with homozygous deletion of exon 7 of the SMN1 gene

    Directory of Open Access Journals (Sweden)

    Žarkov Marija

    2015-01-01

    Full Text Available Background/Aim. Spinal muscular atrophy (SMA is an autosomal recessive disease characterized by degeneration of alpha motor neurons in the spinal cord and the medulla oblongata, causing progressive muscle weakness and atrophy. The aim of this study was to determine association between the SMN2 gene copy number and disease phenotype in Serbian patients with SMA with homozygous deletion of exon 7 of the SMN1 gene. Methods. The patients were identified using regional Serbian hospital databases. Investigated clinical characteristics of the disease were: patients’ gender, age at disease onset, achieved and current developmental milestones, disease duration, current age, and the presence of the spinal deformities and joint contractures. The number of SMN1 and SMN2 gene copies was determined using real-time polymerase chain reaction (PCR. Results. Among 43 identified patients, 37 (86.0% showed homozygous deletion of SMN1 exon 7. One (2.7% of 37 patients had SMA type I with 3 SMN2 copies, 11 (29.7% patients had SMA type II with 3.1 ± 0.7 copies, 17 (45.9% patients had SMA type III with 3.7 ± 0.9 copies, while 8 (21.6% patients had SMA type IV with 4.2 ± 0.9 copies. There was a progressive increase in the SMN2 gene copy number from type II towards type IV (p < 0.05. A higher SMN2 gene copy number was associated with better current motor performance (p < 0.05. Conclusion. In the Serbian patients with SMA, a higher SMN2 gene copy number correlated with less severe disease phenotype. A possible effect of other phenotype modifiers should not be neglected.

  18. Two mechanisms coordinate replication termination by the Escherichia coli Tus–Ter complex

    KAUST Repository

    Pandey, Manjula; Elshenawy, Mohamed; Jergic, Slobodan; Takahashi, Masateru; Dixon, Nicholas E.; Hamdan, Samir; Patel, Smita S.

    2015-01-01

    The Escherichia coli replication terminator protein (Tus) binds to Ter sequences to block replication forks approaching from one direction. Here, we used single molecule and transient state kinetics to study responses of the heterologous phage T7

  19. Effect of high pressurized carbon dioxide on Escherichia coli ...

    African Journals Online (AJOL)

    Carbon dioxide at high pressure can retard microbial growth and sometimes kill microorganisms depending on values of applied pressure, temperature and exposure time. In this study the effect of high pressurised carbon dioxide (HPCD) on Escherichia coli was investigated. Culture of E. coli was subjected to high ...

  20. 7T MRI subthalamic nucleus atlas for use with 3T MRI.

    Science.gov (United States)

    Milchenko, Mikhail; Norris, Scott A; Poston, Kathleen; Campbell, Meghan C; Ushe, Mwiza; Perlmutter, Joel S; Snyder, Abraham Z

    2018-01-01

    Deep brain stimulation (DBS) of the subthalamic nucleus (STN) reduces motor symptoms in most patients with Parkinson disease (PD), yet may produce untoward effects. Investigation of DBS effects requires accurate localization of the STN, which can be difficult to identify on magnetic resonance images collected with clinically available 3T scanners. The goal of this study is to develop a high-quality STN atlas that can be applied to standard 3T images. We created a high-definition STN atlas derived from seven older participants imaged at 7T. This atlas was nonlinearly registered to a standard template representing 56 patients with PD imaged at 3T. This process required development of methodology for nonlinear multimodal image registration. We demonstrate mm-scale STN localization accuracy by comparison of our 3T atlas with a publicly available 7T atlas. We also demonstrate less agreement with an earlier histological atlas. STN localization error in the 56 patients imaged at 3T was less than 1 mm on average. Our methodology enables accurate STN localization in individuals imaged at 3T. The STN atlas and underlying 3T average template in MNI space are freely available to the research community. The image registration methodology developed in the course of this work may be generally applicable to other datasets.

  1. A Canadian Multicentre Case-Control Study of Sporadic Escherichia coli 0157:H7 Infection

    Directory of Open Access Journals (Sweden)

    Donna Holton

    1999-01-01

    Full Text Available OBJECTIVE: To evaluate further risk factors for Escherichia coli 0157:H7 infection including consumer preferences related to the consumption of ground beef and the role of person-to-person transmission of this infection.

  2. Antibiotic susceptibility-resistance profiles of super-shed Escherichia coli O157:H7

    Science.gov (United States)

    Introduction: Escherichia coli O157:H7 (O157) can cause diarrhea and serious secondary sequelae including kidney failure and death in humans. With antibiotics like fosfomycin, colistin and azithromycin, that do not stimulate toxin expression by O157, being considered for treatment of early gastroint...

  3. 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

  4. Assessment of Silent T1-weighted head imaging at 7 T

    Energy Technology Data Exchange (ETDEWEB)

    Costagli, Mauro; Tiberi, Gianluigi; Tosetti, Michela [Imago7 Foundation, Pisa (Italy); IRCCS Stella Maris, Laboratory of Medical Physics and Biotechnologies for Magnetic Resonance, Pisa (Italy); Symms, Mark R. [GE Applied Science Laboratory, Pisa (Italy); Angeli, Lorenzo [University of Pisa, Department of Translational Research and New Technologies in Medicine and Surgery, Pisa (Italy); Kelley, Douglas A.C. [GE Healthcare Technologies, San Francisco, CA (United States); Biagi, Laura [IRCCS Stella Maris, Laboratory of Medical Physics and Biotechnologies for Magnetic Resonance, Pisa (Italy); Farnetani, Andrea [University of Ferrara, Engineering Department, Ferrara (Italy); Materiacustica s.r.l., Ferrara (Italy); Rua, Catarina [University of Pisa, Department of Physics, Pisa (Italy); Donatelli, Graziella [Azienda Ospedaliero-Universitaria Pisana (AOUP), Neuroradiology Unit, Department of Diagnostic and Interventional Radiology, Pisa (Italy); Cosottini, Mirco [Imago7 Foundation, Pisa (Italy); University of Pisa, Department of Translational Research and New Technologies in Medicine and Surgery, Pisa (Italy)

    2016-06-15

    This study aimed to assess the performance of a ''Silent'' zero time of echo (ZTE) sequence for T1-weighted brain imaging using a 7 T MRI system. The Silent sequence was evaluated qualitatively by two neuroradiologists, as well as quantitatively in terms of tissue contrast, homogeneity, signal-to-noise ratio (SNR) and acoustic noise. It was compared to conventional T1-weighted imaging (FSPGR). Adequacy for automated segmentation was evaluated in comparison with FSPGR acquired at 7 T and 1.5 T. Specific absorption rate (SAR) was also measured. Tissue contrast and homogeneity in Silent were remarkable in deep brain structures and in the occipital and temporal lobes. Mean tissue contrast was significantly (p < 0.002) higher in Silent (0.25) than in FSPGR (0.11), which favoured automated tissue segmentation. On the other hand, Silent images had lower SNR with respect to conventional imaging: average SNR of FSPGR was 2.66 times that of Silent. Silent images were affected by artefacts related to projection reconstruction, which nevertheless did not compromise the depiction of brain tissues. Silent acquisition was 35 dB(A) quieter than FSPGR and less than 2.5 dB(A) louder than ambient noise. Six-minute average SAR was <2 W/kg. The ZTE Silent sequence provides high-contrast T1-weighted imaging with low acoustic noise at 7 T. (orig.)

  5. Beneficial effect of a high number of copies of salivary amylase AMY1 gene on obesity risk in Mexican children.

    Science.gov (United States)

    Mejía-Benítez, María A; Bonnefond, Amélie; Yengo, Loïc; Huyvaert, Marlène; Dechaume, Aurélie; Peralta-Romero, Jesús; Klünder-Klünder, Miguel; García Mena, Jaime; El-Sayed Moustafa, Julia S; Falchi, Mario; Cruz, Miguel; Froguel, Philippe

    2015-02-01

    Childhood obesity is a major public health problem in Mexico, affecting one in every three children. Genome-wide association studies identified genetic variants associated with childhood obesity, but a large missing heritability remains to be elucidated. We have recently shown a strong association between a highly polymorphic copy number variant encompassing the salivary amylase gene (AMY1 also known as AMY1A) and obesity in European and Asian adults. In the present study, we aimed to evaluate the association between AMY1 copy number and obesity in Mexican children. We evaluated the number of AMY1 copies in 597 Mexican children (293 obese children and 304 normal weight controls) through highly sensitive digital PCR. The effect of AMY1 copy number on obesity status was assessed using a logistic regression model adjusted for age and sex. We identified a marked effect of AMY1 copy number on reduced risk of obesity (OR per estimated copy 0.84, with the number of copies ranging from one to 16 in this population; p = 4.25 × 10(-6)). The global association between AMY1 copy number and reduced risk of obesity seemed to be mostly driven by the contribution of the highest AMY1 copy number. Strikingly, all children with >10 AMY1 copies were normal weight controls. Salivary amylase initiates the digestion of dietary starch, which is highly consumed in Mexico. Our current study suggests putative benefits of high number of AMY1 copies (and related production of salivary amylase) on energy metabolism in Mexican children.

  6. Diversity of Survival Patterns among Escherichia coli O157:H7 Genotypes Subjected to Food-Related Stress Conditions.

    Science.gov (United States)

    Elhadidy, Mohamed; Álvarez-Ordóñez, Avelino

    2016-01-01

    The purpose of this study was to evaluate the resistance patterns to food-related stresses of Shiga toxin producing Escherichia coli O157:H7 strains belonging to specific genotypes. A total of 33 E. coli O157:H7 strains were exposed to seven different stress conditions acting as potential selective pressures affecting the transmission of E. coli O157:H7 to humans through the food chain. These stress conditions included cold, oxidative, osmotic, acid, heat, freeze-thaw, and starvation stresses. The genotypes used for comparison included lineage-specific polymorphism, Shiga-toxin-encoding bacteriophage insertion sites, clade type, tir (A255T) polymorphism, Shiga toxin 2 subtype, and antiterminator Q gene allele. Bacterial resistance to different stressors was calculated by determining D-values (times required for inactivation of 90% of the bacterial population), which were then subjected to univariate and multivariate analyses. In addition, a relative stress resistance value, integrating resistance values to all tested stressors, was calculated for each bacterial strain and allowed for a ranking-type classification of E. coli O157:H7 strains according to their environmental robustness. Lineage I/II strains were found to be significantly more resistant to acid, cold, and starvation stress than lineage II strains. Similarly, tir (255T) and clade 8 encoding strains were significantly more resistant to acid, heat, cold, and starvation stress than tir (255A) and non-clade 8 strains. Principal component analysis, which allows grouping of strains with similar stress survival characteristics, separated strains of lineage I and I/II from strains of lineage II, which in general showed reduced survival abilities. Results obtained suggest that lineage I/II, tir (255T), and clade 8 strains, which have been previously reported to be more frequently associated with human disease cases, have greater multiple stress resistance than strains of other genotypes. The results from this

  7. Magnetic resonance spectroscopy of the canine brain at 3.0 T and 7.0 T.

    Science.gov (United States)

    Martin-Vaquero, Paula; da Costa, Ronaldo C; Echandi, Rita L; Sammet, Christina L; Knopp, Michael V; Sammet, Steffen

    2012-08-01

    The purpose of this study was to evaluate the feasibility of proton magnetic resonance spectroscopy (1H MRS) to study the concentration of metabolites in the brain of dogs at 3.0 and 7.0 T. Four healthy male beagles were scanned using 3.0 T and 7.0 T human magnetic resonance imaging (MRI) units. The results obtained showed that all dogs had excellent quality spectra for a small (1 cm3) and large (8 cm3) voxel at 3.0 T, whereas only 2 dogs had high quality spectra at 7.0 T due to insufficient water suppression. 1H MRS at 3.0 T appears to be a reliable method to study metabolite concentrations in the canine brain. The development of more advanced water suppression techniques is necessary to improve the results at 7.0 T. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Detection of Escherichia Coli O157:H7 in Fecal Samples in Meat Goats

    Science.gov (United States)

    Mobley, Ray; Madden, Uford; Brooks-Walter, Alexis

    2004-01-01

    Studies have reported the isolation of Escherichia coli (E. coli)O157:H7 from pork, lamb and poultry products, and from other animals including deer, horses, dogs, birds and humans. There is limited or no information on the presence of the organism in goats. The objectives of this study were to determine if E. coli O157:H7 was naturally occurring…

  9. Whole genome DNA copy number changes identified by high density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Huang Jing

    2004-05-01

    Full Text Available Abstract Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs. Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA, to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM and mismatch (MM probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number

  10. Mechanisms for the initiation of bacteriophage T7 DNA replication

    International Nuclear Information System (INIS)

    Fuller, C.W.; Beauchamp, B.B.; Engler, M.J.; Lechner, R.L.; Matson, S.W.; Tabor, S.; White, J.H.; Richardson, C.C.

    1983-01-01

    Genetic analysis of bacteriophage T7 has shown that the products of phage genes 1, 2, 3, 4, 5, and 6 are required for phage DNA synthesis in vivo. T7 RNA polymerase is the translation product of gene 1. This RNA polymerase is required for transcription of most of the phage genome, including genes 2 through 6. T7 RNA polymerase promoters consist of a highly conserved 23-bp DNA sequence. There are 17 such promoters in the T7 DNA molecule, all of which direct transcription from the same strand of the DNA. 70 references, 11 figures

  11. Temperature-Dependent Fermentation of d-Sorbitol in Escherichia coli O157:H7

    OpenAIRE

    Bouvet, O. M. M.; Pernoud, S.; Grimont, P. A. D.

    1999-01-01

    The influence of growth temperature on the ability to ferment d-sorbitol was investigated in Escherichia coli O157:H7. It was found that O157:H7 strains have a temperature-sensitive sorbitol phenotype. d-Sorbitol transport and sorbitol-6-phosphate dehydrogenase activities were expressed in sorbitol-fermenting cells grown at 30°C but only at a low level at 40°C. Sorbitol-positive variants able to transport d-sorbitol were easily selected at 30°C from culture of Sor− E. coli O157:H7 strains.

  12. [Expression of enterotoxigenic Bacteroides fragilis and polyketide synthase gene-expressing Escherichia coli in colorectal adenoma patients].

    Science.gov (United States)

    Xie, L L; Wu, N; Zhu, Y M; Qiu, X Y; Chen, G D; Zhang, L M; Liu, Y L

    2016-03-29

    To investigate the distribution of various bacteria in adenoma tissue of colorectal adenoma (T/CRA), normal colonic mucosa tissue adjacent to the adenoma (N/CRA), and healthy colonic mucosa tissue (N/H) by comparing the number of total bacteria, Bacteroides fragilis (BF), enterotoxigenic Bacteroides fragilis (ETBF), polyketide synthase (pks) gene-expressing Escherichia coli(E.coli)(pks(+) E. coli)among the above 3 types of tissues. A total of 36 patients diagnosed with colorectal adenoma by colonoscopy and pathology in Department of Gastroenterology, Peking University People's Hospital from September 2011 to September 2013 were selected into this study. T/CRA and N/CRA tissues from the 36 patients and N/H tissues from 18 healthy controls were collected for DNA extraction. The number of total bacteria, BF, ETBF, pks(+) E. coli was detected by quantitative real time PCR, and their correlation with colorectal adenoma was analyzed. (1) The number of total bacteria decreased gradually from N/H, N/CRA, to T/CRA, with the median values being 3.18×10(8,) 1.57×10(8,) and 7.91×10(7) copies/g, respectively, and with significant difference among the three groups and between each two groups (all PCRA, to T/CRA, the median values being 6.03×10(5,) 4.28×10(4,) and 5.48×10(3) copies/g, respectively, and with significant difference among the three groups and between each two groups (all PCRA, to T/CRA, the relative expression being 1.73±0.30, 6.15±1.52, and 8.54±1.80, respectively. Significant difference was found between the T/CRA and N/H tissue (P=0.003), but not between any other two groups. (4) The expression of clbB in pks(+) E.coli was highest in T/CRA colonic tissue (2.96±0.28), followed by the N/CRA (2.79±0.19) and N/H tissue (1.06±0.08). Significant difference was found between T/CRA and N/H tissues, as well as between N/CRA and N/H tissues (both PCRA and N/CRA tissues. The number of total bacteria is markedly reduced in the colonic mucosa of CRA patients

  13. Clinical applications of 7 T MRI in the brain

    International Nuclear Information System (INIS)

    Kolk, Anja G. van der; Hendrikse, Jeroen; Zwanenburg, Jaco J.M.; Visser, Fredy; Luijten, Peter R.

    2013-01-01

    This review illustrates current applications and possible future directions of 7 Tesla (7 T) Magnetic Resonance Imaging (MRI) in the field of brain MRI, in clinical studies as well as clinical practice. With its higher signal-to-noise (SNR) and contrast-to-noise ratio (CNR) compared to lower field strengths, high resolution, contrast-rich images can be obtained of diverse pathologies, like multiple sclerosis (MS), brain tumours, aging-related changes and cerebrovascular diseases. In some of these diseases, additional pathophysiological information can be gained compared to lower field strengths. Because of clear depiction of small anatomical details, and higher lesion conspicuousness, earlier diagnosis and start of treatment of brain diseases may become possible. Furthermore, additional insight into the pathogenesis of brain diseases obtained with 7 T MRI could be the basis for new treatment developments. However, imaging at high field comes with several limitations, like inhomogeneous transmit fields, a higher specific absorption rate (SAR) and, currently, extensive contraindications for patient scanning. Future studies will be aimed at assessing the advantages and disadvantages of 7 T MRI over lower field strengths in light of clinical applications, specifically the additional diagnostic and prognostic value of 7 T MRI

  14. Clinical applications of 7 T MRI in the brain

    Energy Technology Data Exchange (ETDEWEB)

    Kolk, Anja G. van der, E-mail: A.G.vanderKolk@umcutrecht.nl [Department of Radiology, University Medical Center Utrecht, Postbox 85500, 3508 GA Utrecht (Netherlands); Hendrikse, Jeroen, E-mail: J.Hendrikse@umcutrecht.nl [Department of Radiology, University Medical Center Utrecht, Postbox 85500, 3508 GA Utrecht (Netherlands); Zwanenburg, Jaco J.M., E-mail: J.J.M.Zwanenburg@umcutrecht.nl [Department of Radiology, University Medical Center Utrecht, Postbox 85500, 3508 GA Utrecht (Netherlands); Image Sciences Institute, University Medical Center Utrecht (Netherlands); Visser, Fredy, E-mail: F.Visser-2@umcutrecht.nl [Department of Radiology, University Medical Center Utrecht, Postbox 85500, 3508 GA Utrecht (Netherlands); Philips Healthcare, Best (Netherlands); Luijten, Peter R., E-mail: P.Luijten@umcutrecht.nl [Department of Radiology, University Medical Center Utrecht, Postbox 85500, 3508 GA Utrecht (Netherlands)

    2013-05-15

    This review illustrates current applications and possible future directions of 7 Tesla (7 T) Magnetic Resonance Imaging (MRI) in the field of brain MRI, in clinical studies as well as clinical practice. With its higher signal-to-noise (SNR) and contrast-to-noise ratio (CNR) compared to lower field strengths, high resolution, contrast-rich images can be obtained of diverse pathologies, like multiple sclerosis (MS), brain tumours, aging-related changes and cerebrovascular diseases. In some of these diseases, additional pathophysiological information can be gained compared to lower field strengths. Because of clear depiction of small anatomical details, and higher lesion conspicuousness, earlier diagnosis and start of treatment of brain diseases may become possible. Furthermore, additional insight into the pathogenesis of brain diseases obtained with 7 T MRI could be the basis for new treatment developments. However, imaging at high field comes with several limitations, like inhomogeneous transmit fields, a higher specific absorption rate (SAR) and, currently, extensive contraindications for patient scanning. Future studies will be aimed at assessing the advantages and disadvantages of 7 T MRI over lower field strengths in light of clinical applications, specifically the additional diagnostic and prognostic value of 7 T MRI.

  15. Humanized CD7 nanobody-based immunotoxins exhibit promising anti-T-cell acute lymphoblastic leukemia potential.

    Science.gov (United States)

    Yu, Yuan; Li, Jialu; Zhu, Xuejun; Tang, Xiaowen; Bao, Yangyi; Sun, Xiang; Huang, Yuhui; Tian, Fang; Liu, Xiaomei; Yang, Lin

    2017-01-01

    Nanobodies, named as VHHs (variable domain of heavy chain of HCAb [heavy-chain antibodies]), are derived from heavy-chain-only antibodies that circulate in sera of camelids. Their exceptional physicochemical properties, possibility of humanization, and unique antigen recognition properties make them excellent candidates for targeted delivery of biologically active components, including immunotoxins. In our previous efforts, we have successfully generated the monovalent and bivalent CD7 nanobody-based immunotoxins, which can effectively trigger the apoptosis of CD7-positive malignant cells. To pursue the possibility of translating those immunotoxins into clinics, we humanized the nanobody sequences (designated as dhuVHH6) as well as further truncated the Pseudomonas exotoxin A (PE)-derived PE38 toxin to produce a more protease-resistant form, which is named as PE-LR, by deleting majority of PE domain II. Three new types of immunotoxins, dhuVHH6-PE38, dVHH6-PE-LR, and dhuVHH6-PE-LR, were successfully constructed. These recombinant immunotoxins were expressed in Escherichia coli and showed that nanobody immunotoxins have the benefits of easy soluble expression in a prokaryotic expression system. Flow cytometry results revealed that all immunotoxins still maintained the ability to bind specifically to CD7-positive T lymphocyte strains without binding to CD7-negative control cells. Laser scanning confocal microscopy revealed that these proteins can be endocytosed into the cytoplasm after binding with CD7-positive cells and that this phenomenon was not observed in CD7-negative cells. WST-8 experiments showed that all immunotoxins retained the highly effective and specific growth inhibition activity in CD7-positive cell lines and primary T-cell acute lymphoblastic leukemia (T-ALL) cells. Further in vivo animal model experiments showed that humanized dhuVHH6-PE38 immunotoxin can tolerate higher doses and extend the survival of NOD-Prkdc em26 Il2rg em26 Nju (NCG) mice

  16. Exposure to high hydrostatic pressure rapidly selects for increased RpoS activity and general stress-resistance in Escherichia coli O157:H7.

    Science.gov (United States)

    Vanlint, Dietrich; Rutten, Nele; Govers, Sander K; Michiels, Chris W; Aertsen, Abram

    2013-04-15

    Exposure to high hydrostatic pressure (HHP) is increasingly being used in food preservation as a non-thermal pasteurization process, and its further implementation necessitates a more thorough understanding of bacterial resistance development and intraspecies variability with regard to inactivation by HHP. In this report, we discovered that exposure to high hydrostatic pressure stress can rapidly select for strongly increased RpoS activity in a hypersensitive Escherichia coli O157:H7 strain (ATCC 43888), leading to a simultaneous increase in HHP and heat resistance. Moreover, the level of RpoS activity correlated well with the original hypersensitivity and the extent of acquired HHP resistance, and extremely HHP-resistant mutants of ATCC 43888 clearly incurred a number of additional RpoS-dependent phenotypes. These findings suggest that implementation of novel processing techniques in the food production chain can readily affect the physiology of food-borne pathogens. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. The occurrence of Escherichia coli O157:H7 in market and abattoir ...

    African Journals Online (AJOL)

    Escherichia coli O157:H7 is a newly emerging pathogen frequently associated with the consumption of foods of bovine origin. The severity of the infections caused by this food borne pathogen in the young and the elderly has had a tremendous impact on human health and food industry. The present study evaluated the ...

  18. Cognitive predictors of copying and drawing from memory of the Rey-Osterrieth complex figure in 7- to 10-year-old children.

    Science.gov (United States)

    Senese, Vincenzo Paolo; De Lucia, Natascia; Conson, Massimiliano

    2015-01-01

    Cognitive models of drawing are mainly based on assessment of copying performance of adults, whereas only a few studies have verified these models in young children. Moreover, developmental investigations have only rarely performed a systematic examination of the contribution of perceptual and representational visuo-spatial processes to copying and drawing from memory. In this study we investigated the role of visual perception and mental representation in both copying and drawing from memory skills in a sample of 227 typically developing children (53% females) aged 7-10 years. Participants underwent a neuropsychological assessment and the Rey-Osterrieth Complex Figure (ROCF). The fit and invariance of the predictive model considering visuo-spatial abilities, working memory, and executive functions were tested by means of hierarchical regressions and path analysis. Results showed that, in a gender invariant way, visual perception abilities and spatial mental representation had a direct effect on copying performance, whereas copying performance was the only specific predictor for drawing from memory. These effects were independent from age and socioeconomic status, and showed that cognitive models of drawing built up for adults could be considered for predicting copying and drawing from memory in children.

  19. High Glucose-Induced Oxidative Stress Increases the Copy Number of Mitochondrial DNA in Human Mesangial Cells

    Directory of Open Access Journals (Sweden)

    Ghada Al-Kafaji

    2013-01-01

    Full Text Available Oxidative damage to mitochondrial DNA (mtDNA has been linked to the pathogenicity of diabetic nephropathy. We tested the hypothesis that mtDNA copy number may be increased in human mesangial cells in response to high glucose-induced reactive oxygen species (ROS to compensate for damaged mtDNA. The effect of manganese superoxide dismutase mimetic (MnTBAP on glucose-induced mtDNA copy number was also examined. The copy number of mtDNA was determined by real-time PCR in human mesangial cells cultured in 5 mM glucose, 25 mM glucose, and mannitol (osmotic control, as well as in cells cultured in 25 mM glucose in the presence and absence of 200 μM MnTBAP. Intracellular ROS was assessed by confocal microscopy and flow cytometry in human mesangial cells. The copy number of mtDNA was significantly increased when human mesangial cells were incubated with 25 mM glucose compared to 5 mM glucose and mannitol. In addition, 25 mM glucose rapidly generated ROS in the cells, which was not detected in 5 mM glucose. Furthermore, mtDNA copy number was significantly decreased and maintained to normal following treatment of cells with 25 mM glucose and MnTBAP compared to 25 mM glucose alone. Inclusion of MnTBAP during 25 mM glucose incubation inhibited mitochondrial superoxide in human mesangial cells. Increased mtDNA copy number in human mesangial cells by high glucose could contribute to increased mitochondrial superoxide, and prevention of mtDNA copy number could have potential in retarding the development of diabetic nephropathy.

  20. Genetic transformation and gene silencing mediated by multiple copies of a transgene in eastern white pine.

    Science.gov (United States)

    Tang, Wei; Newton, Ronald J; Weidner, Douglas A

    2007-01-01

    An efficient transgenic eastern white pine (Pinus strobus L.) plant regeneration system has been established using Agrobacterium tumefaciens strain GV3850-mediated transformation and the green fluorescent protein (gfp) gene as a reporter in this investigation. Stable integration of transgenes in the plant genome of pine was confirmed by polymerase chain reaction (PCR), Southern blot, and northern blot analyses. Transgene expression was analysed in pine T-DNA transformants carrying different numbers of copies of T-DNA insertions. Post-transcriptional gene silencing (PTGS) was mostly obtained in transgenic lines with more than three copies of T-DNA, but not in transgenic lines with one copy of T-DNA. In situ hybridization chromosome analysis of transgenic lines demonstrated that silenced transgenic lines had two or more T-DNA insertions in the same chromosome. These results suggest that two or more T-DNA insertions in the same chromosome facilitate efficient gene silencing in transgenic pine cells expressing green fluorescent protein. There were no differences in shoot differentiation and development between transgenic lines with multiple T-DNA copies and transgenic lines with one or two T-DNA copies.

  1. Whole brain, high resolution spin-echo resting state fMRI using PINS multiplexing at 7 T

    NARCIS (Netherlands)

    Koopmans, P.J.; Boyacioglu, R.; Barth, M.; Norris, David Gordon

    2012-01-01

    This article demonstrates the application of spin-echo EPI for resting state fMRI at 7 T. A short repetition time of 1860 ms was made possible by the use of slice multiplexing which permitted whole brain coverage at high spatial resolution (84 slices of 1.6 mm thickness). Radiofrequency power

  2. Inactivation of Escherichia coli O157:H7 on stainless steel upon exposure to Paenibacillus polymyxa biofilms.

    Science.gov (United States)

    Kim, Seonhwa; Bang, Jihyun; Kim, Hoikyung; Beuchat, Larry R; Ryu, Jee-Hoon

    2013-11-01

    We investigated the potential use of biofilm formed by a competitive-exclusion (CE) microorganism to inactivate Escherichia coli O157:H7 on a stainless steel surface. Five microorganisms showing inhibitory activities against E. coli O157:H7 were isolated from vegetable seeds and sprouts. The microorganism with the greatest antimicrobial activity was identified as Paenibacillus polymyxa (strain T5). In tryptic soy broth (TSB), strain T5 reached a higher population at 25 °C than at 12 or 37 °C without losing inhibitory activity against E. coli O157:H7. When P. polymyxa (6 log CFU/mL) was co-cultured with E. coli O157:H7 (2, 3, 4, or 5 log CFU/mL) in TSB at 25 °C, the number of E. coli O157:H7 decreased significantly within 24h. P. polymyxa formed a biofilm on stainless steel coupons (SSCs) in TSB at 25 °C within 24h, and cells in biofilms, compared to attached cells without biofilm formation, showed significantly increased resistance to a dry environment (43% relative humidity [RH]). With the exception of an inoculum of 4 log CFU/coupon at 100% RH, upon exposure to biofilm formed by P. polymyxa on SSCs, populations of E. coli O157:H7 (2, 4, or 6 log CFU/coupon) were significantly reduced within 48 h. Most notably, when E. coli O157:H7 at 2 log CFU/coupon was applied to SSCs on which P. polymyxa biofilm had formed, it was inactivated within 1h, regardless of RH. These results will be useful when developing strategies using biofilms produced by competitive exclusion microorganisms to inactivate foodborne pathogens in food processing environments. © 2013.

  3. 7 Tesla quantitative hip MRI: T1, T2 and T2* mapping of hip cartilage in healthy volunteers

    Energy Technology Data Exchange (ETDEWEB)

    Lazik, Andrea; Theysohn, Jens M.; Geis, Christina [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Johst, Soeren; Kraff, Oliver [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); Ladd, Mark E. [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); German Cancer Research Center (DKFZ), Medical Physics in Radiology, Heidelberg (Germany); Quick, Harald H. [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); University Hospital Essen, High Field and Hybrid MR Imaging, Essen (Germany)

    2016-05-15

    To evaluate the technical feasibility and applicability of quantitative MR techniques (delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), T2 mapping, T2* mapping) at 7 T MRI for assessing hip cartilage. Hips of 11 healthy volunteers were examined at 7 T MRI with an 8-channel radiofrequency transmit/receive body coil using multi-echo sequences for T2 and T2* mapping and a dual flip angle gradient-echo sequence before (T1{sub 0}) and after intravenous contrast agent administration (T1{sub Gd}; 0.2 mmol/kg Gd-DTPA{sup 2-} followed by 0.5 h of walking and 0.5 h of rest) for dGEMRIC. Relaxation times of cartilage were measured manually in 10 regions of interest. Pearson's correlations between R1{sub delta} = 1/T1{sub Gd} - 1/T1{sub 0} and T1{sub Gd} and between T2 and T2* were calculated. Image quality and the delineation of acetabular and femoral cartilage in the relaxation time maps were evaluated using discrete rating scales. High correlations were found between R1{sub delta} and T1{sub Gd} and between T2 and T2* relaxation times (all p < 0.01). All techniques delivered diagnostic image quality, with best delineation of femoral and acetabular cartilage in the T2* maps (mean 3.2 out of a maximum of 4 points). T1, T2 and T2* mapping of hip cartilage with diagnostic image quality is feasible at 7 T. To perform dGEMRIC at 7 T, pre-contrast T1 mapping can be omitted. (orig.)

  4. Transfer coefficient models for escherichia coli O157:H7 on contacts between beef tissue and high-density polyethylene surfaces.

    Science.gov (United States)

    Flores, Rolando A; Tamplin, Mark L; Marmer, Benne S; Phillips, John G; Cooke, Peter H

    2006-06-01

    Risk studies have identified cross-contamination during beef fabrication as a knowledge gap, particularly as to how and at what levels Escherichia coli O157:H7 transfers among meat and cutting board (or equipment) surfaces. The objectives of this study were to determine and model transfer coefficients (TCs) between E. coli O157:H7 on beef tissue and high-density polyethylene (HDPE) cutting board surfaces. Four different transfer scenarios were evaluated: (i) HDPE board to agar, (ii) beef tissue to agar, (iii) HDPE board to beef tissue to agar, and (iv) beef tissue to HDPE board to agar. Also, the following factors were studied for each transfer scenario: two HDPE surface roughness levels (rough and smooth), two beef tissues (fat and fascia), and two conditions of the initial beef tissue inoculation with E. coli O157:H7 (wet and dry surfaces), for a total of 24 treatments. The TCs were calculated as a function of the plated inoculum and of the cells recovered from the first contact. When the treatments were compared, all of the variables evaluated interacted significantly in determining the TC. An overall TC-per-treatment model did not adequately represent the reduction of the cells on the original surface after each contact and the interaction of the factors studied. However, an exponential model was developed that explained the experimental data for all treatments and represented the recontamination of the surfaces with E. coli O157:H7. The parameters for the exponential model for cross-contamination with E. coli O157:H7 between beef tissue and HDPE surfaces were determined, allowing for the use of the resulting model in quantitative microbial risk assessment.

  5. Escherichia coli O157:H7: Animal Reservoir and Sources of Human Infection

    Science.gov (United States)

    Ferens, Witold A.

    2011-01-01

    Abstract This review surveys the literature on carriage and transmission of enterohemorrhagic Escherichia coli (EHEC) O157:H7 in the context of virulence factors and sampling/culture technique. EHEC of the O157:H7 serotype are worldwide zoonotic pathogens responsible for the majority of severe cases of human EHEC disease. EHEC O157:H7 strains are carried primarily by healthy cattle and other ruminants, but most of the bovine strains are not transmitted to people, and do not exhibit virulence factors associated with human disease. Prevalence of EHEC O157:H7 is probably underestimated. Carriage of EHEC O157:H7 by individual animals is typically short-lived, but pen and farm prevalence of specific isolates may extend for months or years and some carriers, designated as supershedders, may harbor high intestinal numbers of the pathogen for extended periods. The prevalence of EHEC O157:H7 in cattle peaks in the summer and is higher in postweaned calves and heifers than in younger and older animals. Virulent strains of EHEC O157:H7 are rarely harbored by pigs or chickens, but are found in turkeys. The bacteria rarely occur in wildlife with the exception of deer and are only sporadically carried by domestic animals and synanthropic rodents and birds. EHEC O157:H7 occur in amphibian, fish, and invertebrate carriers, and can colonize plant surfaces and tissues via attachment mechanisms different from those mediating intestinal attachment. Strains of EHEC O157:H7 exhibit high genetic variability but typically a small number of genetic types predominate in groups of cattle and a farm environment. Transmission to people occurs primarily via ingestion of inadequately processed contaminated food or water and less frequently through contact with manure, animals, or infected people. PMID:21117940

  6. Canonical Single Nucleotide Polymorphisms (SNPs for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC O157:H7.

    Directory of Open Access Journals (Sweden)

    Sean M Griffing

    Full Text Available The objective of this study was to develop a canonical, parsimoniously-informative SNP panel for subtyping Shiga-toxin producing Escherichia coli (STEC O157:H7 that would be consistent with epidemiological, PFGE, and MLVA clustering of human specimens. Our group had previously identified 906 putative discriminatory SNPs, which were pared down to 391 SNPs based on their prevalence in a test set. The 391 SNPs were screened using a high-throughput form of TaqMan PCR against a set of clinical isolates that represent the most diverse collection of O157:H7 isolates from outbreaks and sporadic cases examined to date. Another 30 SNPs identified by others were also screened using the same method. Two additional targets were tested using standard TaqMan PCR endpoint analysis. These 423 SNPs were reduced to a 32 SNP panel with the almost the same discriminatory value. While the panel partitioned our diverse set of isolates in a manner that was consistent with epidemiological data and PFGE and MLVA phylogenies, it resulted in fewer subtypes than either existing method and insufficient epidemiological resolution in 10 of 47 clusters. Therefore, another round of SNP discovery was undertaken using comparative genomic resequencing of pooled DNA from the 10 clusters with insufficient resolution. This process identified 4,040 potential SNPs and suggested one of the ten clusters was incorrectly grouped. After its removal, there were 2,878 SNPs, of which only 63 were previously identified and 438 occurred across multiple clusters. Among highly clonal bacteria like STEC O157:H7, linkage disequilibrium greatly limits the number of parsimoniously informative SNPs. Therefore, it is perhaps unsurprising that our panel accounted for the potential discriminatory value of numerous other SNPs reported in the literature. We concluded published O157:H7 SNPs are insufficient for effective epidemiological subtyping. However, the 438 multi-cluster SNPs we identified may provide

  7. Evaluation of 39 medical implants at 7.0 T

    Science.gov (United States)

    Feng, David X; McCauley, Joseph P; Morgan–Curtis, Fea K; Salam, Redoan A; Pennell, David R; Loveless, Mary E

    2015-01-01

    Objective: With increased signal to noise ratios, 7.0-T MRI has the potential to contribute unique information regarding anatomy and pathophysiology of a disease. However, concerns for the safety of subjects with metallic medical implants have hindered advancement in this field. The purpose of the present research was to evaluate the MRI safety for 39 commonly used medical implants at 7.0 T. Methods: Selected metallic implants were tested for magnetic field interactions, radiofrequency-induced heating and artefacts using standardized testing techniques. Results: 5 of the 39 implants tested may be unsafe for subjects undergoing MRI at 7.0 T. Conclusion: Implants were deemed either “MR Conditional” or “MR Unsafe” for the 7.0-T MRI environment. Further research is needed to expand the existing database categorizing implants that are acceptable for patients referred for MRI examinations at 7.0 T. Advances in knowledge: Lack of MRI testing for common metallic medical implants limits the translational potential of 7.0-T MRI. For safety reasons, patients with metallic implants are not allowed to undergo a 7.0-T MRI scan, precluding part of the population that can benefit from the detailed resolution of ultra-high-field MRIs. This investigation provides necessary MRI testing of common medical implants at 7.0 T. PMID:26481696

  8. Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis.

    Science.gov (United States)

    Diniz, Marina Gonçalves; Duarte, Alessandra Pires; Villacis, Rolando A; Guimarães, Bruna V A; Duarte, Luiz Cláudio Pires; Rogatto, Sílvia R; Gomez, Ricardo Santiago; Gomes, Carolina Cavaliéri

    2017-05-01

    Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account for their different clinical behaviors. We assessed copy number alterations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) in UA (n = 2), MA (n = 3), and AC (n = 1) using the CytoScan HD Array (Affymetrix) and the BRAFV600E status. RT-qPCR was applied in four selected genes (B4GALT1, BAG1, PKD1L2, and PPP2R5A) covered by rare alterations, also including three MA and four normal oral tissues. Fifty-seven CNAs and cnLOH were observed in the ameloblastomas and six CNAs in the AC. Seven of the CNAs were rare (six in UA and one in MA), four of them encompassing genes (gains of 7q11.21, 1q32.3, and 9p21.1 and loss of 16q23.2). We found positive correlation between rare CNA gene dosage and the expression of B4GALT1, BAG1, PKD1L2, and PPP2R5A. The AC and 1 UA were BRAF wild-type; however, this UA showed rare genomic alterations encompassing genes associated with RAF/MAPK activation. Ameloblastomas show rare CNAs and cnLOH, presenting a specific genomic profile with no overlapping of the rare alterations among UA, MA, and AC. These genomic changes might play a role in tumor evolution and in BRAFV600E-negative tumors. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Single-shot spiral imaging at 7T.

    Science.gov (United States)

    Engel, Maria; Kasper, Lars; Barmet, Christoph; Schmid, Thomas; Vionnet, Laetitia; Wilm, Bertram; Pruessmann, Klaas P

    2018-03-25

    The purpose of this work is to explore the feasibility and performance of single-shot spiral MRI at 7T, using an expanded signal model for reconstruction. Gradient-echo brain imaging is performed on a 7T system using high-resolution single-shot spiral readouts and half-shot spirals that perform dual-image acquisition after a single excitation. Image reconstruction is based on an expanded signal model including the encoding effects of coil sensitivity, static off-resonance, and magnetic field dynamics. The latter are recorded concurrently with image acquisition, using NMR field probes. The resulting image resolution is assessed by point spread function analysis. Single-shot spiral imaging is achieved at a nominal resolution of 0.8 mm, using spiral-out readouts of 53-ms duration. High depiction fidelity is achieved without conspicuous blurring or distortion. Effective resolutions are assessed as 0.8, 0.94, and 0.98 mm in CSF, gray matter and white matter, respectively. High image quality is also achieved with half-shot acquisition yielding image pairs at 1.5-mm resolution. Use of an expanded signal model enables single-shot spiral imaging at 7T with unprecedented image quality. Single-shot and half-shot spiral readouts deploy the sensitivity benefit of high field for rapid high-resolution imaging, particularly for functional MRI and arterial spin labeling. © 2018 International Society for Magnetic Resonance in Medicine.

  10. Copy Counts

    Science.gov (United States)

    Beaumont, Lee R.

    1970-01-01

    The level of difficulty of straight copy, which is used to measure typewriting speed, is influenced by syllable intensity (the average number of syllables per word), stroke intensity (average number of strokes per word), and high-frequency words. (CH)

  11. Recto-anal junction (RAJ) microbiota composition in Escherichia coli O157:H7 shedding cattle

    Science.gov (United States)

    Introduction: Cattle are the asymptomatic reservoirs of Escherichia coli O157:H7 (O157) that tend to preferentially colonize the bovine recto-anal junction (RAJ). Therefore, understanding the taxonomic profile, microbial diversity, and microbiota-O157 interactions at the RAJ could give insights into...

  12. Proliferation of Escherichia coli O157:H7 in soil and hydroponic microgreen production systems

    Science.gov (United States)

    Radish (Raphanus sativus var. longipinnatus) microgreens were produced from seeds inoculated with Escherichia coli O157: H7 using soil substitute and hydroponic production systems. E. coli populations on the edible and inedible parts of harvested microgreen plants and in growth medium were examined....

  13. MR imaging of the temporomandibular joint: comparison between acquisitions at 7.0 T using dielectric pads and 3.0 T.

    Science.gov (United States)

    Kuhn, Felix P; Spinner, Georg; Del Grande, Filippo; Wyss, Michael; Piccirelli, Marco; Erni, Stefan; Pfister, Pascal; Ho, Michael; Sah, Bert-Ram; Filli, Lukas; Ettlin, Dominik A; Gallo, Luigi M; Andreisek, Gustav; Manoliu, Andrei

    2017-01-01

    To qualitatively and quantitatively compare MRI of the temporomandibular joint (TMJ) at 7.0 T using high-permittivity dielectric pads and 3.0 T using a clinical high-resolution protocol. Institutional review board-approved study with written informed consent. 12 asymptomatic volunteers were imaged at 7.0 and 3.0 T using 32-channel head coils. High-permittivity dielectric pads consisting of barium titanate in deuterated suspension were used for imaging at 7.0 T. Imaging protocol consisted of oblique sagittal proton density weighted turbo spin echo sequences. For quantitative analysis, pixelwise signal-to-noise ratio maps of the TMJ were calculated. For qualitative analysis, images were evaluated by two independent readers using 5-point Likert scales. Quantitative and qualitative results were compared using t-tests and Wilcoxon signed-rank tests, respectively. TMJ imaging at 7.0 T using high-permittivity dielectric pads was feasible in all volunteers. Quantitative analysis showed similar signal-to-noise ratio for both field strengths (mean ± SD; 7.0 T, 13.02 ± 3.92; 3.0 T, 14.02 ± 3.41; two-sample t-tests, p = 0.188). At 7.0 T, qualitative analysis yielded better visibility of all anatomical subregions of the temporomandibular disc (anterior band, intermediate zone and posterior band) than 3.0 T (Wilcoxon signed-rank tests, p 3.0 T.

  14. Aptasensors for rapid detection of Escherichia coli O157:H7 and Salmonella typhimurium

    Science.gov (United States)

    Wu, Wen-he; Li, Min; Wang, Yue; Ouyang, Hou-xian; Wang, Lin; Li, Ci-xiu; Cao, Yu-chen; Meng, Qing-he; Lu, Jian-xin

    2012-11-01

    Herein we reported the development of aptamer-based biosensors (aptasensors) based on label-free aptamers and gold nanoparticles (AuNPs) for detection of Escherichia coli ( E. coli) O157:H7 and Salmonella typhimurium. Target bacteria binding aptamers are adsorbed on the surface of unmodified AuNPs to capture target bacteria, and the detection was accomplished by target bacteria-induced aggregation of the aptasensor which is associated as red-to-purple color change upon high-salt conditions. By employing anti- E. coli O157:H7 aptamer and anti- S. typhimurium aptamer, we developed a convenient and rapid approach that could selectively detect bacteria without specialized instrumentation and pretreatment steps such as cell lysis. The aptasensor could detect as low as 105colony-forming units (CFU)/ml target bacteria within 20 min or less and its specificity was 100%. This novel method has a great potential application in rapid detection of bacteria in the near future.

  15. Crystallization and preliminary X-ray diffraction analysis of an Escherichia coli tRNAGly acceptor-stem microhelix

    International Nuclear Information System (INIS)

    Förster, Charlotte; Perbandt, Markus; Brauer, Arnd B. E.; Brode, Svenja; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.

    2006-01-01

    In order to investigate the identity elements of the E. coli tRNA Gly /GlyRS class II system, a tRNA Gly acceptor-stem microhelix was crystallized and a data set was collected to 2.0 Å resolution using synchrotron radiation. The tRNA Gly and glycyl-tRNA synthetase (GlyRS) system is an evolutionary special case within the class II aminoacyl-tRNA synthetases because two divergent types of GlyRS exist: an archaebacterial/human type and an eubacterial type. The tRNA identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of tRNA Gly . To obtain further insight concerning structural investigation of the identity elements, the Escherichia coli seven-base-pair tRNA Gly acceptor-stem helix was crystallized. Data were collected to 2.0 Å resolution using synchrotron radiation. Crystals belong to space group P3 1 21 or P3 2 21, with unit-cell parameters a = b = 35.35, c = 130.82 Å, α = β = 90, γ = 120° and two molecules in the asymmetric unit

  16. Effect of high pressure impact on the survival of Shiga Toxin-producing Escherichia coli ('Big Six' and 0157) in ground beef

    Science.gov (United States)

    High pressure processing (HPP) is a safe and effective technology for improving food safety while maintaining food quality attributes. Non-O157:H7 Shiga Toxin-producing Escherichia coli (STEC) have been increasingly implicated in foodborne illness outbreaks and recalls, and the USDA Food Safety Ins...

  17. Development, Optimization, and Evaluation of a Duplex Droplet Digital PCR Assay To Quantify the T-nos/hmg Copy Number Ratio in Genetically Modified Maize.

    Science.gov (United States)

    Félix-Urquídez, Dalmira; Pérez-Urquiza, Melina; Valdez Torres, José-Benigno; León-Félix, Josefina; García-Estrada, Raymundo; Acatzi-Silva, Abraham

    2016-01-05

    Certified reference materials (CRMs) are required to guarantee the reliability of analytical measurements. The CRMs available in the field of genetically modified organisms (GMOs) are characterized using real-time polymerase chain reaction (qPCR). This technology has limited application, because of its dependence on a calibrant. The objective of this study was to obtain a method with higher metrological quality, to characterize the CRMs for their contents of T-nos/hmg copy number ratio in maize. A duplex droplet digital PCR (ddPCR) assay was developed and optimized by a central composite design. The developed method achieved an absolute limit of detection (LOD) of 11 cP T-nos, a relative LOD of 0.034%, a limit of quantification (LOQ) of 23 cP (relative LOQ of 0.08%), and a dynamic range of 0.08%-100% T-nos/hmg ratio. The specificity and applicability of the assay were established for the analysis of low T-nos concentrations (0.9%) in several corn varieties. The convenience of DNA digestion to reduce measurement bias in the case of multiple-copy binding was confirmed through an enzymatic restriction assay. Given its overall performance, this method can be used to characterize CRM candidates for their contents of T-nos/hmg ratio.

  18. Development, Optimization, and Evaluation of a Duplex Droplet Digital PCR Assay To Quantify the T-nos/hmg Copy Number Ratio in Genetically Modified Maize

    Science.gov (United States)

    2015-01-01

    Certified reference materials (CRMs) are required to guarantee the reliability of analytical measurements. The CRMs available in the field of genetically modified organisms (GMOs) are characterized using real-time polymerase chain reaction (qPCR). This technology has limited application, because of its dependence on a calibrant. The objective of this study was to obtain a method with higher metrological quality, to characterize the CRMs for their contents of T-nos/hmg copy number ratio in maize. A duplex droplet digital PCR (ddPCR) assay was developed and optimized by a central composite design. The developed method achieved an absolute limit of detection (LOD) of 11 cP T-nos, a relative LOD of 0.034%, a limit of quantification (LOQ) of 23 cP (relative LOQ of 0.08%), and a dynamic range of 0.08%–100% T-nos/hmg ratio. The specificity and applicability of the assay were established for the analysis of low T-nos concentrations (0.9%) in several corn varieties. The convenience of DNA digestion to reduce measurement bias in the case of multiple-copy binding was confirmed through an enzymatic restriction assay. Given its overall performance, this method can be used to characterize CRM candidates for their contents of T-nos/hmg ratio. PMID:26605751

  19. Musculoskeletal MRI at 3.0 T and 7.0 T: A comparison of relaxation times and image contrast

    International Nuclear Information System (INIS)

    Jordan, Caroline D.; Saranathan, Manojkumar; Bangerter, Neal K.; Hargreaves, Brian A.; Gold, Garry E.

    2013-01-01

    Objective: The purpose of this study was to measure and compare the relaxation times of musculoskeletal tissues at 3.0 T and 7.0 T, and to use these measurements to select appropriate parameters for musculoskeletal protocols at 7.0 T. Materials and methods: We measured the T 1 and T 2 relaxation times of cartilage, muscle, synovial fluid, bone marrow and subcutaneous fat at both 3.0 T and 7.0 T in the knees of five healthy volunteers. The T 1 relaxation times were measured using a spin-echo inversion recovery sequence with six inversion times. The T 2 relaxation times were measured using a spin-echo sequence with seven echo times. The accuracy of both the T 1 and T 2 measurement techniques was verified in phantoms at both magnetic field strengths. We used the measured relaxation times to help design 7.0 T musculoskeletal protocols that preserve the favorable contrast characteristics of our 3.0 T protocols, while achieving significantly higher resolution at higher SNR efficiency. Results: The T 1 relaxation times in all tissues at 7.0 T were consistently higher than those measured at 3.0 T, while the T 2 relaxation times at 7.0 T were consistently lower than those measured at 3.0 T. The measured relaxation times were used to help develop high resolution 7.0 T protocols that had similar fluid-to-cartilage contrast to that of the standard clinical 3.0 T protocols for the following sequences: proton-density-weighted fast spin-echo (FSE), T 2 -weighted FSE, and 3D-FSE-Cube. Conclusion: The T 1 and T 2 changes were within the expected ranges. Parameters for musculoskeletal protocols at 7.0 T can be optimized based on these values, yielding improved resolution in musculoskeletal imaging with similar contrast to that of standard 3.0 T clinical protocols

  20. The positioning logic and copy number control of genes in bacteria under stress

    Science.gov (United States)

    Zhang, Qiucen; Austin, Robert; Vyawahare, Saurabh; Lau, Alexandra

    2013-03-01

    Escherichia coli (E. coli) cells when challenged with sublethal concentrations of the genotoxic antibiotic ciprofloxacin cease to divide and form long filaments which contain multiple bacterial chromosomes. These filaments are individual mesoscopic environmental niches which provide protection for a community of chromosomes (as opposed to cells) under mutagenic stress and can provide an evolutionary fitness advantage within the niche. We use comparative genomic hybridization to show that the mesoscopic niche evolves within 20 minutes of ciprofloxacin exposure via replication of multiple copies of genes expressing ATP dependent transporters. We show that this rapid genomic amplification is done in a time efficient manner via placement of the genes encoding the pumps near the origin of replication on the bacterial chromosome. The de-amplification of multiple copies back to the wild type number is a function of the duration is a function of the ciprofloxacin exposure duration: the longer the exposure, the slower the removal of the multiple copies. The project described was supported by the National Science Foundation and the National Cancer Institute

  1. On the efficient bio-incorporation of 5-hydroxy-tryptophan in recombinant proteins expressed in Escherichia coli with T7 RNA polymerase-based vectors.

    Science.gov (United States)

    Oliveira-Souza, Wellington P; Bronze, Fellipe; Broos, Jaap; Marcondes, Marcelo F M; Oliveira, Vitor

    2017-10-21

    Biosynthetic incorporation of non-canonic amino acids is an attractive strategy to introduce new properties in recombinant proteins. Trp analogs can be incorporated in recombinant proteins replacing regular Trp during protein translation into a Trp-auxotrophic cell host. This straightforward method however, is limited to few analogs recognized and accepted by the cellular protein production machinery. 5-hydroxy-tryptophan (5OH-Trp) can be bio-incorporated using E. coli as expression host however; we have experienced very low incorporation yields - amount of protein containing regular Trp/amount of protein containing the Trp analog - during expressions of 5OH-Trp labeled proteins. Furthermore, this low incorporation yield were verified especially when the widely-used vectors based on the T7 RNA polymerase were used. Testing different 5OH-Trp incorporation protocols we verified that in these T7-based systems, the production of the T7 RNA polymerase is driven by the same elements - lac promoter/IPTG - as the target protein. Consequently, the bio-incorporation of the 5OH-Trp residues also occurs in this crucial enzyme, but, the produced T7 RNA polymerase labeled with 5OH-Trp is inactive or much less active. In the present work, we describe an efficient method to overcome this mentioned problem and bio-incorporate 5OH-Trp in proteins expressed in E. coli., using vectors based on the T7 RNA polymerase-T7 promoter. The two-step induction protocol here described showed incorporation efficiencies of 5OH-Trp higher than 90%. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Chromosomal Fragmentation in "Escherichia Coli": Its Absence in "mutT" Mutants and Its Mechanisms in "seqA" Mutants

    Science.gov (United States)

    Rotman, Ella Rose

    2009-01-01

    Chromosomal fragmentation in "Escherichia coli" is a lethal event for the cell unless mended by the recombinational repair proteins RecA, RecBCD, and RuvABC. Certain mutations exacerbate problems that cause the cell to be dependent on the recombinational repair proteins for viability. We tested whether the absence of the MutT protein caused…

  3. Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop.

    Science.gov (United States)

    Stephen, Preyesh; Ye, Sheng; Zhou, Ming; Song, Jian; Zhang, Rongguang; Wang, En-Duo; Giegé, Richard; Lin, Sheng-Xiang

    2018-05-25

    Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNA Arg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure-function understanding in prokaryotic tRNA Arg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNA Arg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNA Arg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Development and characterization of a magnetic bead-quantum dot nanoparticles based assay capable of Escherichia coli O157:H7 quantification

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Gha-Young [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States); Son, Ahjeong, E-mail: ason@auburn.edu [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States)

    2010-09-10

    The development and characterization of a magnetic bead (MB)-quantum dot (QD) nanoparticles based assay capable of quantifying pathogenic bacteria is presented here. The MB-QD assay operates by having a capturing probe DNA selectively linked to the signaling probe DNA via the target genomic DNA (gDNA) during DNA hybridization. The signaling probe DNA is labeled with fluorescent QD{sub 565} which serves as a reporter. The capturing probe DNA is conjugated simultaneously to a MB and another QD{sub 655}, which serve as a carrier and an internal standard, respectively. Successfully captured target gDNA is separated using a magnetic field and is quantified via a spectrofluorometer. The use of QDs (i.e., QD{sub 565}/QD{sub 655}) as both a fluorescence label and an internal standard increased the sensitivity of the assay. The passivation effect and the molar ratio between QD and DNA were optimized. The MB-QD assay demonstrated a detection limit of 890 zeptomolar (i.e., 10{sup -21} mol L{sup -1}) concentration for the linear single stranded DNA (ssDNA). It also demonstrated a detection limit of 87 gene copies for double stranded DNA (dsDNA) eaeA gene extracted from pure Escherichia coli (E. coli) O157:H7 culture. Its corresponding dynamic range, sensitivity, and selectivity were also presented. Finally, the bacterial gDNA of E. coli O157:H7 was used to highlight the MB-QD assay's ability to detect below the minimum infective dose (i.e., 100 organisms) of E. coli O157:H7 in water environment.

  5. iTRAQ-Based Proteomic Analysis of Sublethally Injured Escherichia coli O157:H7 Cells Induced by High Pressure Carbon Dioxide

    Directory of Open Access Journals (Sweden)

    Xiufang Bi

    2017-12-01

    Full Text Available High pressure carbon dioxide (HPCD could cause sublethally injured cells (SICs, which may cause food poisoning and spoilage during food storage and limit its application. Therefore, the formation of SICs of Escherichia coli O157:H7 was investigated by isobaric tag for relative and absolute quantification (iTRAQ proteomic methods in this study for better controlling the SICs induced by HPCD. A total of 2,446 proteins was identified by iTRAQ, of which 93 and 29 were significantly differentially expressed in the SICs compared with live control cells (CKL and dead control cells (CKD, respectively. Among the 93 differentially expressed proteins (DEP in the SICs compared with CKL, 65 proteins showed down-regulation and 28 showed up-regulation. According to the comprehensive proteome coverage analysis, the SICs survived under HPCD by reducing carbohydrate decomposing, lipid transport and metabolism, amino acid transport and metabolism, transcription and translation, DNA replication and repair. Besides, the SICs showed stress response, DNA damage response and an increased carbohydrate transport, peptidoglycan synthesis and disulfide bond formation to HPCD. Among the 29 DEP in the SICs compared with CKD, 12 proteins showed down-regulation and 17 showed up-regulation. According to the comprehensive proteome coverage analysis, the SICs survived under HPCD by accumulation of cell protective agents like carbohydrates and amino acids, and decreasing transcription and translation activities. Results showed that the formation of the SICs with low metabolic activity and high survival ability was a survival strategy for E. coli O157:H7 against HPCD.

  6. Carvacrol and p-cymene inactivate Escherichia coli O157:H7 in apple juice

    Directory of Open Access Journals (Sweden)

    Roller Sibel

    2005-06-01

    Full Text Available Abstract Background Outbreaks of food poisoning associated with drinking un-pasteurised apple juice contaminated with enterohaemorrhagic Escherichia coli O157:H7 are a cause of serious illness and occasionally death. Whilst a well-established heat process (pasteurisation will readily eliminate the pathogen, some consumers are demanding more fresh-like foods that have not been subjected to processing methods that are perceived as severe and may lead to loss of flavour and vitamins. Therefore, alternative methods are being investigated to replace pasteurisation and improve the safety of minimally-processed juices. The addition of natural antimicrobial substances such as the phenolic substances carvacrol and p-cymene (derived from the essential oils of herbs and spices provides a potential new route to assure safety and extend the shelf-life of raw fruit juices. The aim of this study was to evaluate the addition of very low concentrations (0.25–1.25 mM of carvacrol and p-cymene both individually and in combination as a novel means of controlling Escherichia coli O157:H7 in un-pasteurised apple juice. Results When inoculated at a level of 4 log CFU/ml into un-pasteurised apple juice (pH 3.20 ± 0.06, Escherichia coli O157:H7 survived for up to 3 and 19 days at 25° and 4°C, respectively. Treatment of the juice with 1.25 mM carvacrol or p-cymene reduced the numbers of E. coli O157:H7 to undetectable levels within 1–2 days at both storage temperatures. The effective concentrations of carvacrol could be reduced even further by combining it at 0.5 mM with cymene at 0.25 mM. The phenolic compounds were biocidal against both spoilage yeasts and E. coli O157:H7 thereby increasing the shelf-life and improving the safety of un-pasteurised apple juice, particularly when stored at chill temperatures. Conclusion The results showed that the natural antimicrobial compounds carvacrol and p-cymene could potentially be used to extend the shelf life and improve

  7. Lethality Prediction for Escherichia Coli O157:H7 and Uropathogenic E. coli in Ground Chicken Treated with High Pressure Processing and Trans-Cinnamaldehyde.

    Science.gov (United States)

    Sheen, Shiowshuh; Huang, Chi-Yun; Ramos, Rommel; Chien, Shih-Yung; Scullen, O Joseph; Sommers, Christopher

    2018-03-01

    Pathogenic Escherichia coli, intestinal (O157:H7) as well as extraintestinal types (for example, Uropathogenic E. coli [UPEC]) are commonly found in many foods including raw chicken meat. The resistance of E. coli O157:H7 to UPEC in chicken meat under the stresses of high hydrostatic Pressure (HHP, also known as HPP-high pressure processing) and trans-cinnamaldehyde (an essential oil) was investigated and compared. UPEC was found slightly less resistant than O157:H7 in our test parameter ranges. With the addition of trans-cinnamaldehyde as an antimicrobial to meat, HPP lethality enhanced both O157:H7 and UPEC inactivation. To facilitate the predictive model development, a central composite design (CCD) was used to assess the 3-parameter effects, that is, pressure (300 to 400 MPa), trans-cinnamaldehyde dose (0.2 to 0.5%, w/w), and pressure-holding time (15 to 25 min), on the inactivation of E. coli O157:H7 and UPEC in ground chicken. Linear models were developed to estimate the lethality of E. coli O157:H7 (R 2 = 0.86) and UPEC (R 2 = 0.85), as well as dimensionless nonlinear models. All models were validated with data obtained from separated CCD combinations. Because linear models of O157:H7 and UPEC had similar R 2 and the significant lethality difference of CCD points was only 9 in 20; all data were combined to generate models to include both O157:H7 and UPEC. The results provide useful information/tool to predict how pathogenic E. coli may survive HPP in the presence of trans-cinnamaldehyde and to achieve a great than 5 log CFU/g reduction in chicken meat. The models may be used for process optimization, product development and to assist the microbial risk assessment. The study provided an effective means to reduce the high hydrostatic pressure level with incorporation of antimicrobial compound to achieve a 5-log reduction of pathogenic E. coli without damaging the raw meat quality. The developed models may be used to predict the high pressure processing

  8. Incidence of Escherichia coli O157:H7 in Thailand

    International Nuclear Information System (INIS)

    Sukhumungoon, P.

    2015-01-01

    Entero hemorrhagic Escherichia coli (EHEC) especially serotype O157:H7 is one of the important food-borne pathogens because it is able to produce crucial toxins Shiga. However, the outbreak of this organism in Thailand has not been reported. Antibody to O157 antigen was detected in some Thai populations and Shiga toxin-producing E. coli were detected in low numbers of clinical specimens. Interestingly, some E. coli that showed positive to O157 fimbriae probe and lack of virulence gene were isolated from certain patients and one isolate of E. coli O157:H7 which possessed stx1, stx2v was detected in a normal child. In addition, the incidence of E. coli O157:H7 strains were monitored by the samples from cattle and retail beef in Thailand although their inability to produce toxins or produce in a low concentration was demonstrated. This review discusses the incidences of E. coli O157 in clinical and environmental samples of Thailand including the transmission possibility of this bacterium across the Thai border through food trade. (author)

  9. Structure–function relations in the NTPase domain of the antiviral tRNA ribotoxin Escherichia coli PrrC

    International Nuclear Information System (INIS)

    Meineke, Birthe; Shuman, Stewart

    2012-01-01

    Breakage of tRNA by Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection. Expression of EcoPrrC is cytocidal in yeast, signifying that PrrC ribotoxicity crosses phylogenetic domain boundaries. EcoPrrC consists of an N-terminal NTPase module that resembles ABC transporters and a C-terminal nuclease module that is sui generis. PrrC homologs are prevalent in many other bacteria. Here we report that Haemophilus influenzae PrrC is toxic in E. coli and yeast. To illuminate structure–activity relations, we conducted a new round of mutational analysis of EcoPrrC guided by primary structure conservation among toxic PrrC homologs. We indentify 17 candidate active site residues in the NTPase module that are essential for toxicity in yeast when EcoPrrC is expressed at high gene dosage. Their functions could be educed by integrating mutational data with the atomic structure of the transition-state complex of a homologous ABC protein.

  10. Structure-function relations in the NTPase domain of the antiviral tRNA ribotoxin Escherichia coli PrrC

    Energy Technology Data Exchange (ETDEWEB)

    Meineke, Birthe; Shuman, Stewart, E-mail: s-shuman@ski.mskcc.org

    2012-06-05

    Breakage of tRNA by Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection. Expression of EcoPrrC is cytocidal in yeast, signifying that PrrC ribotoxicity crosses phylogenetic domain boundaries. EcoPrrC consists of an N-terminal NTPase module that resembles ABC transporters and a C-terminal nuclease module that is sui generis. PrrC homologs are prevalent in many other bacteria. Here we report that Haemophilus influenzae PrrC is toxic in E. coli and yeast. To illuminate structure-activity relations, we conducted a new round of mutational analysis of EcoPrrC guided by primary structure conservation among toxic PrrC homologs. We indentify 17 candidate active site residues in the NTPase module that are essential for toxicity in yeast when EcoPrrC is expressed at high gene dosage. Their functions could be educed by integrating mutational data with the atomic structure of the transition-state complex of a homologous ABC protein.

  11. A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase•tRNAHis pair.

    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.

  12. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae).

    Science.gov (United States)

    Weitemier, Kevin; Straub, Shannon C K; Fishbein, Mark; Liston, Aaron

    2015-01-01

    Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual's consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the "noncoding" ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming).

  13. Determination of gamma radiation dose to the destruction of Escherichia coli O157: H7 in hamburger

    International Nuclear Information System (INIS)

    Orejuela Chirinos, Rodolfo Raul

    1999-01-01

    Escherichia coli O157:H7 has been incriminated in several foodborne outbreaks due to the consumption of different kinds of foods. Among these, hamburgers are the most common. Irradiation process is an effective method for food preservation because it causes no significant change in organoleptic and nutritional food characteristics and destroys pathogens and spoilage microorganisms. Hamburgers and nutrient broth inoculated with Escherichia coli O157:H7 were submitted to gamma irradiation ( 60 Co) treatment, with doses ranging from 0,0 to 0,7 kGy in order to calculate the D 10 for this bacteria in these substrate. The D 10 for the pathogen nutrient broth ranged from 0.08 kGy to 0.10 kGy and in hamburger from 0.11 kGy to 0.21 kGy. Considering the highest D 10 value in hamburger, a dose of 0,8 kGy would not change the sensorial characteristics of the product, and would reduce the population of E. coli O157:H7 in 4 cycles logarithmic. (author)

  14. High incidence of recurrent copy number variants in patients with isolated and syndromic Müllerian aplasia.

    Science.gov (United States)

    Nik-Zainal, Serena; Strick, Reiner; Storer, Mekayla; Huang, Ni; Rad, Roland; Willatt, Lionel; Fitzgerald, Tomas; Martin, Vicki; Sandford, Richard; Carter, Nigel P; Janecke, Andreas R; Renner, Stefan P; Oppelt, Patricia G; Oppelt, Peter; Schulze, Christine; Brucker, Sara; Hurles, Matthew; Beckmann, Matthias W; Strissel, Pamela L; Shaw-Smith, Charles

    2011-03-01

    Congenital malformations involving the Müllerian ducts are observed in around 5% of infertile women. Complete aplasia of the uterus, cervix, and upper vagina, also termed Müllerian aplasia or Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome, occurs with an incidence of around 1 in 4500 female births, and occurs in both isolated and syndromic forms. Previous reports have suggested that a proportion of cases, especially syndromic cases, are caused by variation in copy number at different genomic loci. In order to obtain an overview of the contribution of copy number variation to both isolated and syndromic forms of Müllerian aplasia, copy number assays were performed in a series of 63 cases, of which 25 were syndromic and 38 isolated. A high incidence (9/63, 14%) of recurrent copy number variants in this cohort is reported here. These comprised four cases of microdeletion at 16p11.2, an autism susceptibility locus not previously associated with Müllerian aplasia, four cases of microdeletion at 17q12, and one case of a distal 22q11.2 microdeletion. Microdeletions at 16p11.2 and 17q12 were found in 4/38 (10.5%) cases with isolated Müllerian aplasia, and at 16p11.2, 17q12 and 22q11.2 (distal) in 5/25 cases (20%) with syndromic Müllerian aplasia. The finding of microdeletion at 16p11.2 in 2/38 (5%) of isolated and 2/25 (8%) of syndromic cases suggests a significant contribution of this copy number variant alone to the pathogenesis of Müllerian aplasia. Overall, the high incidence of recurrent copy number variants in all forms of Müllerian aplasia has implications for the understanding of the aetiopathogenesis of the condition, and for genetic counselling in families affected by it.

  15. FOXP3+ Tregs and B7-H1+/PD-1+ T lymphocytes co-infiltrate the tumor tissues of high-risk breast cancer patients: Implication for immunotherapy

    International Nuclear Information System (INIS)

    Ghebeh, Hazem; Barhoush, Eman; Tulbah, Asma; Elkum, Naser; Al-Tweigeri, Taher; Dermime, Said

    2008-01-01

    Recent studies have demonstrated a direct involvement of B7-H1, PD-1 and FOXP3 molecules in the immune escape of cancer. B7-H1 is an inhibitory molecule that binds to PD-1 on T lymphocytes, while FOXP3 is a marker for regulatory T cells (T regs ). We have previously demonstrated the association of B7-H1-expressing T infiltrating lymphocytes (TIL) with high-risk breast cancer patients while other studies reported the involvement of FOXP3+ T regs as a bad prognostic factor in breast tumors. Although the co-existence between the two types of cells has been demonstrated in vitro and animal models, their relative infiltration and correlation with the clinicopathological parameters of cancer patients have not been well studied. Therefore, we investigated TIL-expressing the B7-H1, PD-1, and FOXP3 molecules, in the microenvironment of human breast tumors and their possible association with the progression of the disease. Using immunohistochemistry, tumor sections from 62 breast cancer patients were co-stained for B7-H1, PD-1 and FOXP3 molecules and their expression was statistically correlated with factors known to be involved in the progression of the disease. A co-existence of B7-H1 + T lymphocytes and FOXP3 + T regs was evidenced by the highly significant correlation of these molecules (P < .0001) and their expression by different T lymphocyte subsets was clearly demonstrated. Interestingly, concomitant presence of FOXP3 + T regs , B7-H1 + and PD-1 + TIL synergistically correlated with high histological grade (III) (P < .001), estrogen receptor negative status (P = .017), and the presence of severe lymphocytic infiltration (P = .022). Accumulation of TIL-expressing such inhibitory molecules may deteriorate the immunity of high-risk breast cancer patients and this should encourage vigorous combinatorial immunotherapeutic approaches targeting T regs and B7-H1/PD-1 molecules

  16. Primer aislamiento de Escherichia coli O157:H7 Enterohemorrágica en el Perú

    Directory of Open Access Journals (Sweden)

    Blanca Huapaya C

    2001-01-01

    Full Text Available En Febrero del año 2001 como parte del "Estudio transversal de los agentes etiológicos de diarrea aguda" en la Macrorregión Sur del país, el Laboratorio Referencial de Tacna aisló una cepa procedente de una muestra de heces de un lactante de 11 meses de edad con un cuadro de diarrea disentérica, identificándola como Escherichia coli O157. Esta cepa fue confirmada y caracterizada en el Instituto Nacional de Salud como E. coli O157:H7 toxina shiga tipo II, siendo el primer aislamiento reportado de Escherichia coli enterohemorrágica en el Perú.

  17. Effects of thermosonication on the fate of Escherichia coli O157:H7 and Salmonella Enteritidis in mango juice.

    Science.gov (United States)

    Kiang, W-S; Bhat, R; Rosma, A; Cheng, L-H

    2013-04-01

    In this study, the effects of thermosonication and thermal treatment on Escherichia coli O157:H7 and Salmonella Enteritidis in mango juice were investigated at 50 and 60°C. Besides, nonlethal injury of Salm. Enteritidis after both treatments was also examined. The highest inactivation was attained with thermosonication at 60°C. The inactivation rate was different for both pathogens, and Salm. Enteritidis was found to be more sensitive to thermosonication than E. coli O157:H7. Salmonella Enteritidis was recovered in all treated samples, except those subjected to more than 5-min thermosonication at 60°C. It was found that the introduction of high-intensity ultrasound enhanced the inactivation of pathogens compared to thermal treatment alone. On the other hand, Salm. Enteritidis was detected in a number of samples following incubation in universal pre-enrichment broth, but no growth was detected after incubation in mango juice. Fruit juices are commonly heat treated to inactivate micro-organisms and enzymes. However, excessive heat treatments may result in undesirable changes in juice quality. Treatment by power ultrasound, a nonthermal technology, may be an alternative processing technique to pasteurize fruit juices. This study highlights the effectiveness of thermosonication in inactivating Escherichia coli O157:H7 and Salmonella Enteritidis in mango juice. © 2012 The Society for Applied Microbiology.

  18. Proofreading in vivo: Editing of homocysteine by methionyl-tRNA synthetase in Escherichia coli

    International Nuclear Information System (INIS)

    Jakubowski, H.

    1990-01-01

    Previous in vitro studies have established a pre-transfer proofreading mechanism for editing of homocysteine by bacterial methionyl-, isoleucyl-, and valyl-tRNA synthetases. The unusual feature of the editing is the formation of a distinct compound, homocysteine thiolactone. Now, two-dimensional TLC analysis of 35S-labeled amino acids extracted from cultures of the bacterium Escherichia coli reveals that the thiolactone is also synthesized in vivo. In E. coli, the thiolactone is made from homocysteine in a reaction catalyzed by methionyl-tRNA synthetase. One molecule of homocysteine is edited as thiolactone per 109 molecules of methionine incorporated into protein in vivo. These results not only directly demonstrate that the adenylate proofreading pathway for rejection of misactivated homocysteine operates in vivo in E. coli but, in general, establish the importance of error-editing mechanisms in living cells

  19. Targeted sequencing identifies associations between IL7R-JAK mutations and epigenetic modulators in T-cell acute lymphoblastic leukemia

    Science.gov (United States)

    Vicente, Carmen; Schwab, Claire; Broux, Michaël; Geerdens, Ellen; Degryse, Sandrine; Demeyer, Sofie; Lahortiga, Idoya; Elliott, Alannah; Chilton, Lucy; La Starza, Roberta; Mecucci, Cristina; Vandenberghe, Peter; Goulden, Nicholas; Vora, Ajay; Moorman, Anthony V.; Soulier, Jean; Harrison, Christine J.; Clappier, Emmanuelle; Cools, Jan

    2015-01-01

    T-cell acute lymphoblastic leukemia is caused by the accumulation of multiple oncogenic lesions, including chromosomal rearrangements and mutations. To determine the frequency and co-occurrence of mutations in T-cell acute lymphoblastic leukemia, we performed targeted re-sequencing of 115 genes across 155 diagnostic samples (44 adult and 111 childhood cases). NOTCH1 and CDKN2A/B were mutated/deleted in more than half of the cases, while an additional 37 genes were mutated/deleted in 4% to 20% of cases. We found that IL7R-JAK pathway genes were mutated in 27.7% of cases, with JAK3 mutations being the most frequent event in this group. Copy number variations were also detected, including deletions of CREBBP or CTCF and duplication of MYB. FLT3 mutations were rare, but a novel extracellular mutation in FLT3 was detected and confirmed to be transforming. Furthermore, we identified complex patterns of pairwise associations, including a significant association between mutations in IL7R-JAK genes and epigenetic regulators (WT1, PRC2, PHF6). Our analyses showed that IL7R-JAK genetic lesions did not confer adverse prognosis in T-cell acute lymphoblastic leukemia cases enrolled in the UK ALL2003 trial. Overall, these results identify interconnections between the T-cell acute lymphoblastic leukemia genome and disease biology, and suggest a potential clinical application for JAK inhibitors in a significant proportion of patients with T-cell acute lymphoblastic leukemia. PMID:26206799

  20. Synthesis of bacteriophage-coded gene products during infection of Escherichia coli with amber mutants of T3 and T7 defective in gene 1

    DEFF Research Database (Denmark)

    Issinger, O G; Hausmann, R

    1973-01-01

    During nonpermissive infection by a T7 amber mutant in gene 1 (phage RNA polymerase-deficient), synthesis of the products of the phage genes 3 (endonuclease), 3, 5 (lysozyme), 5 (DNA polymerase), and 17 (serum blocking power) was shown to occur at about half the rate as during wild-type infection...

  1. Estimating the Probability of Traditional Copying, Conditional on Answer-Copying Statistics.

    Science.gov (United States)

    Allen, Jeff; Ghattas, Andrew

    2016-06-01

    Statistics for detecting copying on multiple-choice tests produce p values measuring the probability of a value at least as large as that observed, under the null hypothesis of no copying. The posterior probability of copying is arguably more relevant than the p value, but cannot be derived from Bayes' theorem unless the population probability of copying and probability distribution of the answer-copying statistic under copying are known. In this article, the authors develop an estimator for the posterior probability of copying that is based on estimable quantities and can be used with any answer-copying statistic. The performance of the estimator is evaluated via simulation, and the authors demonstrate how to apply the formula using actual data. Potential uses, generalizability to other types of cheating, and limitations of the approach are discussed.

  2. Musculoskeletal MRI at 3.0 T and 7.0 T: a comparison of relaxation times and image contrast.

    Science.gov (United States)

    Jordan, Caroline D; Saranathan, Manojkumar; Bangerter, Neal K; Hargreaves, Brian A; Gold, Garry E

    2013-05-01

    The purpose of this study was to measure and compare the relaxation times of musculoskeletal tissues at 3.0 T and 7.0 T, and to use these measurements to select appropriate parameters for musculoskeletal protocols at 7.0 T. We measured the T₁ and T₂ relaxation times of cartilage, muscle, synovial fluid, bone marrow and subcutaneous fat at both 3.0 T and 7.0 T in the knees of five healthy volunteers. The T₁ relaxation times were measured using a spin-echo inversion recovery sequence with six inversion times. The T₂ relaxation times were measured using a spin-echo sequence with seven echo times. The accuracy of both the T₁ and T₂ measurement techniques was verified in phantoms at both magnetic field strengths. We used the measured relaxation times to help design 7.0 T musculoskeletal protocols that preserve the favorable contrast characteristics of our 3.0 T protocols, while achieving significantly higher resolution at higher SNR efficiency. The T₁ relaxation times in all tissues at 7.0 T were consistently higher than those measured at 3.0 T, while the T₂ relaxation times at 7.0 T were consistently lower than those measured at 3.0 T. The measured relaxation times were used to help develop high resolution 7.0 T protocols that had similar fluid-to-cartilage contrast to that of the standard clinical 3.0 T protocols for the following sequences: proton-density-weighted fast spin-echo (FSE), T₂-weighted FSE, and 3D-FSE-Cube. The T₁ and T₂ changes were within the expected ranges. Parameters for musculoskeletal protocols at 7.0 T can be optimized based on these values, yielding improved resolution in musculoskeletal imaging with similar contrast to that of standard 3.0 T clinical protocols. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  3. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae

    Directory of Open Access Journals (Sweden)

    Kevin Weitemier

    2015-01-01

    Full Text Available Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%. Most nrDNA positions (91% were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming.

  4. The Pai-associated leuX specific tRNA5(Leu) affects type 1fimbriation in pathogenic Escherichia coli by control of FimB recombinase expression

    DEFF Research Database (Denmark)

    Ritter, A.; Gally, D.; Olsen, Peter Bjarke

    1997-01-01

    The uropathogenic Escherichia coli strain 536 (06:K15:H31) carries two large chromosomalpathogenicity islands (Pais). Both Pais are flanked by tRNA genes. Spontaneous deletion of Pai IIresults in truncation of the leuX tRNA5Leu gene. This tRNA is required for the expression of type 1fimbriae (Fim...

  5. Nonsense and sense suppression abilities of original and derivative Methanosarcina mazei pyrrolysyl-tRNA synthetase-tRNA(Pyl pairs in the Escherichia coli BL21(DE3 cell strain.

    Directory of Open Access Journals (Sweden)

    Keturah A Odoi

    Full Text Available Systematic studies of nonsense and sense suppression of the original and three derivative Methanosarcina mazei PylRS-tRNA(Pyl pairs and cross recognition between nonsense codons and various tRNA(Pyl anticodons in the Escherichia coli BL21(DE3 cell strain are reported. tRNA(CUA(Pyl is orthogonal in E. coli and able to induce strong amber suppression when it is co-expressed with pyrrolysyl-tRNA synthetase (PylRS and charged with a PylRS substrate, N(ε-tert-butoxycarbonyl-L-lysine (BocK. Similar to tRNA(CUA(Pyl, tRNA(UUA(Pyl is also orthogonal in E. coli and can be coupled with PylRS to genetically incorporate BocK at an ochre mutation site. Although tRNA(UUA(Pyl is expected to recognize a UAG codon based on the wobble hypothesis, the PylRS-tRNA(UUA(Pyl pair does not give rise to amber suppression that surpasses the basal amber suppression level in E. coli. E. coli itself displays a relatively high opal suppression level and tryptophan (Trp is incorporated at an opal mutation site. Although the PylRS-tRNA(UCA(Pyl pair can be used to encode BocK at an opal codon, the pair fails to suppress the incorporation of Trp at the same site. tRNA(CCU(Pyl fails to deliver BocK at an AGG codon when co-expressed with PylRS in E. coli.

  6. Polyamine stress at high pH in Escherichia coli K-12

    Directory of Open Access Journals (Sweden)

    Tate Daniel P

    2005-10-01

    Full Text Available Abstract Background Polyamines such as spermine and spermidine are required for growth of Escherichia coli; they interact with nucleic acids, and they bind to ribosomes. Polyamines block porins and decrease membrane permeability, activities that may protect cells in acid. At high concentrations, however, polyamines impair growth. They impair growth more severely at high pH, probably due to their increased uptake as membrane-permeant weak bases. The role of pH is critical in understanding polyamine stress. Results The effect of polyamines was tested on survival of Escherichia coli K-12 W3110 in extreme acid or base (pH conditions outside the growth range. At pH 2, 10 mM spermine increased survival by 2-fold, and putrescine increased survival by 30%. At pH 9.8, however, E. coli survival was decreased 100-fold by 10 mM spermine, putrescine, cadaverine, or spermidine. At pH 8.5, spermine decreased the growth rate substantially, whereas little effect was seen at pH 5.5. Spermidine required ten-fold higher concentrations to impair growth. On proteomic 2-D gels, spermine and spermidine caused differential expression of 31 different proteins. During log-phase growth at pH 7.0, 1 mM spermine induced eight proteins, including PykF, GlpK, SerS, DeaD, OmpC and OmpF. Proteins repressed included acetate-inducible enzymes (YfiD, Pta, Lpd as well as RapA (HepA, and FabB. At pH 8.5, spermine induced additional proteins: TnaA, OmpA, YrdA and NanA (YhcJ and also repressed 17 proteins. Four of the proteins that spermine induced (GlpK, OmpA, OmpF, TnaA and five that were repressed (Lpd, Pta, SucB, TpiA, YfiD show similar induction or repression, respectively, in base compared to acid. Most of these base stress proteins were also regulated by spermidine, but only at ten-fold higher concentration (10 mM at high pH (pH 8.5. Conclusion Polyamines increase survival in extreme acid, but decrease E. coli survival in extreme base. Growth inhibition by spermine and

  7. 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 ...

  8. Survival of bioluminescent Listeria monocytogenes and Escherichia coli O157:H7 in soft cheeses.

    Science.gov (United States)

    Ramsaran, H; Chen, J; Brunke, B; Hill, A; Griffiths, M W

    1998-07-01

    Pasteurized and raw milks that had been inoculated at 10(4) cfu/ml with bioluminescent strains of Listeria monocytogenes and Escherichia coli O157:H7 were used in the manufacture of Camembert and Feta cheeses with or without nisin-producing starter culture. Survival of both organisms was determined during the manufacture and storage of Camembert and Feta cheeses at 2 +/- 1 degree C for 65 and 75 d, respectively. Bacterial bioluminescence was used as an indicator to enumerate the colonies plated on selective Listeria agar and on MacConkey agar. Escherichia coli O157:H7 survived the manufacturing process of both cheeses and was present at the end of the storage period in greater numbers than in the initial inoculum. At the end of 75 d of storage, E. coli O157:H7 was found in the brine of Feta cheese. The counts of L. monocytogenes increased as the pH of the Camembert cheese increased, and there were significant differences between the counts from samples taken from the inside and the counts from samples obtained near the surface of the cheese. The Feta cheese that contained nisin was the only cheese in which L. monocytogenes was at the level of the initial inoculum after 75 d of storage.

  9. High-transport current density up to 30 T in bulk YBa2Cu3O7 and the critical angle effect

    International Nuclear Information System (INIS)

    Ekin, J.W.; Salama, K.; Selvamanickam, V.

    1991-01-01

    Measurements of the dc transport critical current of oriented-grained YBa 2 Cu 3 O 7 have been made using high quality Ag contacts and a high-current sample mount. The critical- current density J c at 77 K for mutually perpendicular current and magnetic field B in the a,b plane is 8 kA/cm 2 at 8 T, decreasing gradually to 3.7 kA/cm 2 at 20 T, and remaining over 1 kA/cm 2 out to 30 T. High magnetic field measurements of J c as a function of the angle θ of B with respect to the c axis are also reported. In contrast to earlier results at lower fields ( c vs θ curve with a head-and-shoulders shape, consisting of a sharp peak (''head'') 2 planes, and a wide (30 degree at 9 T, for example) shoulder region on either side of B perpendicular c, where the transport J c remains high and constant. Beyond the shoulder region, however, the transport J c decreases sharply, giving rise to the concept of a critical field angle for application design, defined by the minima in d 2 J c /dθ 2 at the edge of the shoulders

  10. CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Ishikawa Shumpei

    2006-02-01

    Full Text Available Abstract Background DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell. Results We describe a novel algorithm called CARAT (Copy Number Analysis with Regression And Tree that uses probe intensity information to infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated for a subset of SNPs using quantitative PCR and allelic TaqMan reactions with several human breast cancer cell lines. The sensitivity and specificity of the algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well as a test set of normal individuals. Results from the algorithm show a high degree of agreement with results from independent verification methods. Conclusion Overall, CARAT automatically detects regions with copy number variations and assigns a significance score to each alteration as well as generating allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail into the structure of genome wide alterations that can contribute to allelic imbalance.

  11. Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344T during Growth in Beer

    Science.gov (United States)

    Pittet, Vanessa; Phister, Trevor G.; Ziola, Barry

    2013-01-01

    Growth of specific lactic acid bacteria in beer leads to spoiled product and economic loss for the brewing industry. Microbial growth is typically inhibited by the combined stresses found in beer (e.g., ethanol, hops, low pH, minimal nutrients); however, certain bacteria have adapted to grow in this harsh environment. Considering little is known about the mechanisms used by bacteria to grow in and spoil beer, transcriptome sequencing was performed on a variant of the beer-spoilage organism Pediococcus claussenii ATCC BAA-344T (Pc344-358). Illumina sequencing was used to compare the transcript levels in Pc344-358 growing mid-exponentially in beer to those in nutrient-rich MRS broth. Various operons demonstrated high gene expression in beer, several of which are involved in nutrient acquisition and overcoming the inhibitory effects of hop compounds. As well, genes functioning in cell membrane modification and biosynthesis demonstrated significantly higher transcript levels in Pc344-358 growing in beer. Three plasmids had the majority of their genes showing increased transcript levels in beer, whereas the two cryptic plasmids showed slightly decreased gene expression. Follow-up analysis of plasmid copy number in both growth environments revealed similar trends, where more copies of the three non-cryptic plasmids were found in Pc344-358 growing in beer. Transcriptome sequencing also enabled the addition of several genes to the P . claussenii ATCC BAA-344T genome annotation, some of which are putatively transcribed as non-coding RNAs. The sequencing results not only provide the first transcriptome description of a beer-spoilage organism while growing in beer, but they also highlight several targets for future exploration, including genes that may have a role in the general stress response of lactic acid bacteria. PMID:24040005

  12. Inferring Variation in Copy Number Using High Throughput Sequencing Data in R.

    Science.gov (United States)

    Knaus, Brian J; Grünwald, Niklaus J

    2018-01-01

    Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori . Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR . This method is based on the relative frequency of each allele (in both genic and non-genic regions) sequenced at heterozygous positions throughout a genome. These heterozygous positions are summarized by using arbitrarily sized windows of heterozygous positions, binning the allele frequencies, and selecting the bin with the greatest abundance of positions. This provides a non-parametric summary of the frequency that alleles were sequenced at. The method is applicable to organisms that have reference genomes that consist of full chromosomes or sub-chromosomal contigs. In contrast to other software designed to detect copy number variation, our method does not rely on an assumption of base ploidy, but instead infers it. We validated these approaches with the model system of Saccharomyces cerevisiae and applied it to the oomycete Phytophthora infestans , both known to vary in copy number. This functionality has been incorporated into the current release of the R package vcfR to provide modular and flexible methods to investigate copy number variation in genomic projects.

  13. 48 CFR 6302.25 - Copies of papers (Rule 25).

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false Copies of papers (Rule 25). 6302.25 Section 6302.25 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION BOARD OF CONTRACT APPEALS RULES OF PROCEDURE 6302.25 Copies of papers (Rule 25). When books, records, papers, or...

  14. Restriction of phage T4 internal protein I mutants by a strain of Escherichia coli

    International Nuclear Information System (INIS)

    Black, L.W.; Abremski, K.

    1974-01-01

    Phage T4 internal protein I(IPI), a small (ca, 10,000 MW), basic protein injected into the host with the phage DNA, is not required for infection of most hosts, but mutants defective in IPI are restricted by at least one naturally occurring strain of Escherichia coli, CT 596 (CT). Phages lacking IPI (IPI - ) appear to inject their DNA and bind it to the membrane of CT cells as well as wild-type phage T4 does, but shutoff of host protein synthesis, initiation of T4 protein synthesis, and cell killing are abnormal in the IPI - mutant infected CT host. The injection of IPI appears to be important in allowing T4 DNA to carry out early steps involved in takeover of this host. Restriction of IPI - phage growth by CT cells appears to be due, at least in part, to a defective prophage it harbors which renders the host resistant to successful infection by phage T4 which lack IPI or rII functions. Bacteria cured of this prophage can be infected by mutants defective in these functions. The resistance of CT cells to other coliphages, and the question of T-even phage internal protein diversity are discussed. (U.S.)

  15. Purification and characterization of the d-xylose isomerase gene from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Ho, N W.Y.; Rosenfeld, S; Stevis, P; Tsao, G T

    1983-11-01

    A DNA fragment containing both the Escherichia coli D-xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) gene and the D-xylulokinase (ATP: D-xylulose 5-phosphotransferase, EC 2.7.1.17) gene has been cloned on an E. coli plasmid. The D-xylose isomerase gene was separated from the D-xylulokinase gene by the construction of a new deletion plasmid, pLX7. The D-xylose isomerase gene cloned on pLX7 was found still to be an intact gene. The precise location of the D-xylose isomerase gene on the plasmid pLX7 was further determined by the construction of two more plasmids, pLX8 and pLX9. This is believed to be the first D-xylose isomerase gene that has been isolated and extensively purified from any organism. D-Xylose isomerase, the enzyme product of the D-xylose isomerase gene, is responsible for the conversion of D-xylose to D-xylulose, as well as D-glucose to D-fructose. It is widely believed that yeast cannot ferment D-xylose to ethanol primarily because of the lack of D-xylose isomerase in yeast. D-Xylose isomerase (also known as D-glucose isomerase) is also used for the commercial production of high-fructose syrups. The purification of the D-xylose isomerase gene may lead to the following industrial applications: (1) cloning and expression of the gene in yeast to make the latter organism capable of directly fermenting D-xylose to ethanol, and (2) cloning of the gene on a high-copy-number plasmid in a proper host to overproduce the enzyme, which should have a profound impact on the high-fructose syrup technology. 14 references.

  16. rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus

    Science.gov (United States)

    Jansen, M. D.; Bosch, T.; Jansen, W. T. M.; Schouls, L.; Jonker, M. J.; Boel, C. H. E.

    2016-01-01

    The distinct epidemiology of original hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) and early community-associated MRSA (CA-MRSA) is largely unexplained. S. aureus carries either five or six rRNA operon copies. Evidence is provided for a scenario in which MRSA has adapted to the hospital environment by rRNA operon loss (six to five copies) due to antibiotic pressure. Early CA-MRSA, in contrast, results from wild-type methicillin-susceptible S. aureus (MSSA) that acquired mecA without loss of an rRNA operon. Of the HA-MRSA isolates (n = 77), 67.5% had five rRNA operon copies, compared to 23.2% of the CA-MRSA isolates (n = 69) and 7.7% of MSSA isolates (n = 195) (P operon copies. For all subsets, a correlation between resistance profile and rRNA copy number was found. Furthermore, we showed that in vitro antibiotic pressure may result in rRNA operon copy loss. We also showed that without antibiotic pressure, S. aureus isolates containing six rRNA copies are more fit than isolates with five copies. We conclude that HA-MRSA and cystic fibrosis isolates most likely have adapted to an environment with high antibiotic pressure by the loss of an rRNA operon copy. This loss has facilitated resistance development, which promoted survival in these niches. However, strain fitness decreased, which explains their lack of success in the community. In contrast, CA-MRSA isolates retained six rRNA operon copies, rendering them fitter and thereby able to survive and spread in the community. PMID:27671073

  17. Detection of Escherichia coli O157:H7 in the beef marketed in Malaysia.

    Science.gov (United States)

    Radu, S; Abdul Mutalib, S; Rusul, G; Ahmad, Z; Morigaki, T; Asai, N; Kim, Y B; Okuda, J; Nishibuchi, M

    1998-03-01

    Twelve strains of Escherichia coli O157:H7 were isolated from 9 of 25 beef samples purchased from retail stores in Malaysia. These strains produced Shiga toxin 2 with or without Shiga toxin 1 and had the eae gene and a 60-MDa plasmid. The antibiograms and the profiles of the arbitrarily primed PCR of the strains were diverse, suggesting that the strains may have originated from diverse sources.

  18. Protein abundance profiling of the Escherichia coli cytosol

    DEFF Research Database (Denmark)

    Ishihama, Y.; Schmidt, T.; Rappsilber, J.

    2008-01-01

    sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI...... approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal...

  19. Dynamics of chromosome segregation in Escherichia coli

    DEFF Research Database (Denmark)

    Nielsen, Henrik Jørck

    2007-01-01

    Since the 1960’es the conformation and segregation of the chromosome in Escherichia coli has been a subject of interest for many scientists. However, after 40 years of research, we still know incredibly little about how the chromosome is organized inside the cell, how it manages to duplicate...... this incredibly big molecule and separate the two daughter chromosomes and how it makes sure that the daughter cells receives one copy each. The fully extended chromosome is two orders of magnitude larger than the cell in which it is contained. Hence the chromosome is heavily compacted in the cell...

  20. ELECTROPHORETIC MOBILITIES OF ESCHERICHIA COLI 0157:H7 AND WILD-TYPE ESCHERICHIA COLI STRAINS

    Science.gov (United States)

    The electrophoretic mobility (EPM) of a number of human-virulent and "wild-type" Escherichia coli strains in phosphate buffered water was measured. The impact of pH, ionic strength, cation type (valence) and concentration, and bacterial strain on the EPM was investigated. Resul...

  1. Copy number variation in glutathione-S-transferase T1 and M1 predicts incidence and 5-year survival from prostate and bladder cancer, and incidence of corpus uteri cancer in the general population

    DEFF Research Database (Denmark)

    Nørskov, M S; Frikke-Schmidt, R; Bojesen, S E

    2011-01-01

    Glutathione-S-transferase T1 (GSTT1) and GSTM1 detoxify carcinogens and thus potentially contribute to inter-individual susceptibility to cancer. We determined the ability of GST copy number variation (CNV) to predict the risk of cancer in the general population. Exact copy numbers of GSTT1 and G...

  2. Spin-four N=7 W-Supergravity: S-fold and Double Copy Construction arXiv

    CERN Document Server

    Ferrara, Sergio

    In the present investigation we consider the possibility of having new massive, higher spin W-supergravity theories, which do not exist as four-dimensional perturbative models. These theories are based on a double copy construction of two supersymmetric field theories, where at least one factor is given by a N=3 field theory, which is a non-perturbative S-fold of N=4 super Yang-Mills theory. In this way, we can obtain as S-folds a new N=7 (corresponding to 28 supercharges) W-supergravity and its N=7 W-superstring counterpart, which both do not exist as four-dimensional perturbative models with an (effective) Langrangian description. The resulting field resp. string theory does not contain any massless states, but instead a massive higher spin-four supermultiplet of the N=7 supersymmetry algebra. Furthermore we also construct a four-dimensional heterotic S-fold with N=3 supersymmetry. It again does not exist as perturbative heterotic string model and can be considered as the heterotic counterpart of the N=3 su...

  3. Allelic recombination between distinct genomic locations generates copy number diversity in human β-defensins

    Science.gov (United States)

    Bakar, Suhaili Abu; Hollox, Edward J.; Armour, John A. L.

    2009-01-01

    β-Defensins are small secreted antimicrobial and signaling peptides involved in the innate immune response of vertebrates. In humans, a cluster of at least 7 of these genes shows extensive copy number variation, with a diploid copy number commonly ranging between 2 and 7. Using a genetic mapping approach, we show that this cluster is at not 1 but 2 distinct genomic loci ≈5 Mb apart on chromosome band 8p23.1, contradicting the most recent genome assembly. We also demonstrate that the predominant mechanism of change in β-defensin copy number is simple allelic recombination occurring in the interval between the 2 distinct genomic loci for these genes. In 416 meiotic transmissions, we observe 3 events creating a haplotype copy number not found in the parent, equivalent to a germ-line rate of copy number change of ≈0.7% per gamete. This places it among the fastest-changing copy number variants currently known. PMID:19131514

  4. High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer.

    Science.gov (United States)

    Garcia-Fernàndez, J; Bayascas-Ramírez, J R; Marfany, G; Muñoz-Mármol, A M; Casali, A; Baguñà, J; Saló, E

    1995-05-01

    Several DNA sequences similar to the mariner element were isolated and characterized in the platyhelminthe Dugesia (Girardia) tigrina. They were 1,288 bp long, flanked by two 32 bp-inverted repeats, and contained a single 339 amino acid open-reading frame (ORF) encoding the transposase. The number of copies of this element is approximately 8,000 per haploid genome, constituting a member of the middle-repetitive DNA of Dugesia tigrina. Sequence analysis of several elements showed a high percentage of conservation between the different copies. Most of them presented an intact ORF and the standard signals of actively expressed genes, which suggests that some of them are or have recently been functional transposons. The high degree of similarity shared with other mariner elements from some arthropods, together with the fact that this element is undetectable in other planarian species, strongly suggests a case of horizontal transfer between these two distant phyla.

  5. Humanized CD7 nanobody-based immunotoxins exhibit promising anti-T-cell acute lymphoblastic leukemia potential

    Directory of Open Access Journals (Sweden)

    Yu Y

    2017-03-01

    all immunotoxins still maintained the ability to bind specifically to CD7-positive T lymphocyte strains without binding to CD7-negative control cells. Laser scanning confocal microscopy revealed that these proteins can be endocytosed into the cytoplasm after binding with CD7-positive cells and that this phenomenon was not observed in CD7-negative cells. WST-8 experiments showed that all immunotoxins retained the highly effective and specific growth inhibition activity in CD7-positive cell lines and primary T-cell acute lymphoblastic leukemia (T-ALL cells. Further in vivo animal model experiments showed that humanized dhuVHH6-PE38 immunotoxin can tolerate higher doses and extend the survival of NOD-Prkdcem26Il2rgem26Nju (NCG mice transplanted with CEM cells without any obvious decrease in body weight. Further studies on NCG mice model with patient-derived T-ALL cells, dhuVHH6-PE38 treatment, significantly prolonged mice survival with ~40% survival improvement. However, it was also noticed that although dhuVHH6-PE-LR showed strong antitumor effect in vitro, its in vivo antitumor efficacy was disappointing. Conclusion: We have successfully constructed a targeted CD7 molecule-modified nanobody (CD7 molecule-improved nanobody immunotoxin dhuVHH6-PE38 and demonstrated its potential for treating CD7-positive malignant tumors, especially T-cell acute lymphoblastic leukemia. Keywords: CD7, humanized nanobody, T-cell acute lymphoblastic leukemia, patient-derived xenograft model, recombinant immunotoxins, Pseudomonas exotoxin A

  6. Clinically feasible NODDI characterization of glioma using multiband EPI at 7 T

    Directory of Open Access Journals (Sweden)

    Qiuting Wen

    2015-01-01

    Full Text Available Recent technological progress in the multiband echo planer imaging (MB EPI technique enables accelerated MR diffusion weighted imaging (DWI and allows whole brain, multi-b-value diffusion imaging to be acquired within a clinically feasible time. However, its applications at 7 T have been limited due to B1 field inhomogeneity and increased susceptibility artifact. It is an ongoing debate whether DWI at 7 T can be performed properly in patients, and a systematic SNR comparison for multiband spin-echo EPI between 3 T and 7 T has not been methodically studied. The goal of this study was to use MB EPI at 7 T in order to obtain 90-directional multi-shell DWI within a clinically feasible acquisition time for patients with glioma. This study included an SNR comparison between 3 T and 7 T, and the application of B1 mapping and distortion correction procedures for reducing the impact of variations in B0 and B1. The optimized multiband sequence was applied in 20 patients with glioma to generate both DTI and NODDI maps for comparison of values in tumor and normal appearing white matter (NAWM. Our SNR analysis showed that MB EPI at 7 T was comparable to that at 3 T, and the data quality acquired in patients was clinically acceptable. NODDI maps provided unique contrast within the T2 lesion that was not seen in anatomical images or DTI maps. Such contrast may reflect the complexity of tissue compositions associated with disease progression and treatment effects. The ability to consistently obtain high quality diffusion data at 7 T will contribute towards the implementation of a comprehensive brain MRI examination at ultra-high field.

  7. The Escherichia coli O157:H7 bovine rumen fluid proteome reflects adaptive bacterial responses

    OpenAIRE

    Kudva, Indira T; Stanton, Thaddeus B; Lippolis, John D

    2014-01-01

    Background To obtain insights into Escherichia coli O157:H7 (O157) survival mechanisms in the bovine rumen, we defined the growth characteristics and proteome of O157 cultured in rumen fluid (RF; pH 6.0-7.2 and low volatile fatty acid content) obtained from rumen-fistulated cattle fed low protein content “maintenance diet” under diverse in vitro conditions. Results Bottom-up proteomics (LC-MS/MS) of whole cell-lysates of O157 cultured under anaerobic conditions in filter-sterilized RF (fRF; d...

  8. Gauge field copies

    International Nuclear Information System (INIS)

    Bollini, C.G.; Giambiagi, J.J.; Tiomno, J.

    1979-01-01

    The construction of field strength copies without any gauge constraint is discussed. Several examples are given, one of which is not only a field strength copy but also (at the same time) a 'current copy'. (author) [pt

  9. Genetic analysis of attTn7, the transposon Tn7 attachment site in Escherichia coli, using a novel M13-based transduction assay.

    Science.gov (United States)

    Qadri, M I; Flores, C C; Davis, A J; Lichtenstein, C P

    1989-05-05

    The large (14 kb; kb = 10(3) bases) bacterial transposon, Tn7 (encoding resistance to trimethoprim and streptomycin/spectinomycin), has unusual properties. Like other elements, Tn7 transposes with low efficiency and low target-site specificity, but Tn7 also transposes, with high frequency in a unique orientation, to a preferred "attachment" site, called attTn7, in the Escherichia coli chromosome and similarly into plasmids containing attTn7. We developed a novel bacteriophage M13-based assay system to measure the transposition frequency of Tn7 to M13mp phage vectors containing attTn7 on a cloned 1 kb fragment of chromosomal DNA. Phage harvested from a Tn7 donor strain were used to infect recipient bacteria with selection for trimethoprim resistance. Transposition frequency, expressed as the number of trimethoprim-resistant colonies per plaque-forming unit, was found to be approximately 10(-4) to M13mp::attTn7, in contrast to 10(-10) to M13mp recombinants with approximately 1 kb insertions of other, "generic brand", DNA. By deletion analysis of M13mp::attTn7, we show that attTn7 is contained within a 64 base-pair region; sequences adjacent to the actual insertion site and encoding the carboxy terminus of the glmS gene are required. This assay also provided evidence for transposition immunity conferred by the right end of Tn7.

  10. Synergistic interaction in dual-species biofilms formation by Escherichia coli O157:H7 and Ralstonia spp

    Science.gov (United States)

    Introduction: Ralstonia spp., a heterotrophic bacterium that are isolated from produce processing environments as part of the native microflora, have strong potentials for formaing biofilms on various surfaces. When co-cultured, Escherichia coli O157:H7 (EcO157) and Ralstonia spp. displayed a synerg...

  11. Detección de Escherichia coli O157: H7 en carne picada fresca y hamburguesas congeladas Escherichia coli O157: H7 detection in fresh ground beef and hamburgers

    Directory of Open Access Journals (Sweden)

    M. A. Marzocca

    2006-03-01

    Full Text Available Escherichia coli O157:H7 es un patógeno emergente asociado a enfermedades transmitidas por alimentos. En el año 1982 fue reconocido por primera vez, en los Estados Unidos, como causante de dos brotes de colitis hemorrágica. Hoy se sabe que la mayoría de los casos de síndrome urémico hemolítico son ocasionados por este microorganismo. El objetivo del trabajo fue detectar su presencia en carne picada fresca y hamburguesas congeladas, muestras obtenidas en puntos de venta de nuestra cadena de supermercados en un total de 37 y 43, respectivamente, en el período comprendido entre abril de 2003 y agosto de 2004. Las mismas fueron procesadas utilizando el caldo selectivo para enriquecimiento EC modificado conteniendo novobiocina, seguido de la aplicación de un método de inmunocaptura (TECRA E. COLI O157 IMMUNOCAPTURE TM ECOICM 20, y posterior aislamiento en agar MacConkey sorbitol suplementado con cefixima y telurito de potasio y un medio cromogénico. Las cepas sospechosas fueron caracterizadas a genotípicamente mediante la detección de los genes de virulencia stx1, stx2, eaeA y EHEC-hlyA por PCR e hibridación con sondas genéticas, b fenotípicamente mediante la determinación del serotipo, sensibilidad a los antimicrobianos por el método de difusión de Kirby-Bauer y producción de Stx por ensayo de citotoxicidad específica en células Vero. Se aisló E. coli O157:H7 en una sola muestra de carne picada fresca (2,7% caracterizada como gen eae (+/stx2/EHEC-hlyA.Escherichia coli O157:H7 is an emergent pathogen associated with food transmitted diseases. In 1982, Escherichia coli 0157:H7 was for the first time identified as the cause of two hemorrhagic colitis outbreaks in the United States. It is now well known that most cases of hemolytic uremic syndrome are caused by these bacteria. The objective of this work was to detect the microorganism in fresh ground beef and hamburgers. From April 2003 to August 2004 samples were taken at sale

  12. Experimental electromagnetic effects on the model organism Escherichia coli and the bacteriophage T4

    Science.gov (United States)

    Lisiewski, Darlene Mildred

    This experimentally-based work was designed to answer the research question as to whether the phenomenon of nuclear magnetic resonance (NMR) can produce observable effects upon the bacterial virus activity of T4, with such activity demonstrated through the infection of its host bacterium Escherichia coli. The biological samples were placed for three hours within a coil antenna assembly propagating oscillating fields of radio frequency electromagnetic energy generated at the frequency of 5.6 MHz, and set at right angles within a magnetic field of 1450 gauss (recognizing such conditions are not set for the maximum effective resonance for hydrogen nuclei). The laboratory technique of plaque formation was the basis upon which the statistically tested data were compiled. Exposure of the bacterium alone exhibited an increase in viral activity over the control group (40--68% higher numbers of plaque formation), while exposure of T4 alone saw a decrease (approximately 23%) in infection rates. Depending on the protocol, placement of both T4 and E. coli into the coil assembly saw a decrease of either approximately 50% or 42% in infection rates. Future research must address identification of the effects being observed.

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

    Science.gov (United States)

    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

  14. 29 CFR 1921.17 - Service; copies of documents and pleadings.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 7 2010-07-01 2010-07-01 false Service; copies of documents and pleadings. 1921.17 Section 1921.17 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION... LONGSHOREMEN'S AND HARBOR WORKERS' COMPENSATION ACT Miscellaneous § 1921.17 Service; copies of documents and...

  15. Exploring structure and function of sensory cortex with 7T MRI.

    Science.gov (United States)

    Schluppeck, Denis; Sanchez-Panchuelo, Rosa-Maria; Francis, Susan T

    2018-01-01

    In this paper, we present an overview of 7T magnetic resonance imaging (MRI) studies of the detailed function and anatomy of sensory areas of the human brain. We discuss the motivation for the studies, with particular emphasis on increasing the spatial resolution of functional MRI (fMRI) using reduced field-of-view (FOV) data acquisitions. MRI at ultra-high-field (UHF) - defined here as 7T and above - has several advantages over lower field strengths. The intrinsic signal-to-noise ratio (SNR) of images is higher at UHF, and coupled with the increased blood-oxygen-level-dependent (BOLD) signal change, this results in increased BOLD contrast-to-noise ratio (CNR), which can be exploited to improve spatial resolution or detect weaker signals. Additionally, the BOLD signal from the intra-vascular (IV) compartment is relatively diminished compared to lower field strengths. Together, these properties make 7T functional MRI an attractive proposition for high spatial specificity measures. But with the advantages come some challenges. For example, increased vulnerability to susceptibility-induced geometric distortions and signal loss in EPI acquisitions tend to be much larger. Some of these technical issues can be addressed with currently available tools and will be discussed. We highlight the key methodological considerations for high resolution functional and structural imaging at 7 T. We then present recent data using the high spatial resolution available at UHF in studies of the visual and somatosensory cortex to highlight promising developments in this area. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. An 8-channel transceiver 7-channel receive RF coil setup for high SNR ultrahigh-field MRI of the shoulder at 7T.

    Science.gov (United States)

    Rietsch, Stefan H G; Pfaffenrot, Viktor; Bitz, Andreas K; Orzada, Stephan; Brunheim, Sascha; Lazik-Palm, Andrea; Theysohn, Jens M; Ladd, Mark E; Quick, Harald H; Kraff, Oliver

    2017-12-01

    In this work, we present an 8-channel transceiver (Tx/Rx) 7-channel receive (Rx) radiofrequency (RF) coil setup for 7 T ultrahigh-field MR imaging of the shoulder. A C-shaped 8-channel Tx/Rx coil was combined with an anatomically close-fitting 7-channel Rx-only coil. The safety and performance parameters of this coil setup were evaluated on the bench and in phantom experiments. The 7 T MR imaging performance of the shoulder RF coil setup was evaluated in in vivo measurements using a 3D DESS, a 2D PD-weighted TSE sequence, and safety supervision based on virtual observation points. Distinct SNR gain and acceleration capabilities provided by the additional 7-channel Rx-only coil were demonstrated in phantom and in vivo measurements. The power efficiency indicated good performance of each channel and a maximum B 1 + of 19 μT if the hardware RF power limits of the MR system were exploited. MR imaging of the shoulder was demonstrated with clinically excellent image quality and submillimeter spatial resolution. The presented 8-channel transceiver 7-channel receive RF coil setup was successfully applied for in vivo 7 T MRI of the shoulder providing a clear SNR gain vs the transceiver array without the additional receive array. Homogeneous images across the shoulder region were obtained using 8-channel subject-specific phase-only RF shimming. © 2017 American Association of Physicists in Medicine.

  17. Vibrational spectra and lattice instabilities in the high-T/sub c/ superconductors YBa2Cu3O7 and GdBa2Cu3O7

    International Nuclear Information System (INIS)

    Bozovic, I.; Mitzi, D.; Beasley, M.

    1987-01-01

    The exceptionally high T/sub c/ of layered cuprates was proposed recently as originating from electronically driven structural instabilities. We have studied the infrared and Raman spectra of YBa 2 Cu 3 O/sub 7-//sub δ/ and GdBa 2 Cu 3 O/sub 7-//sub δ/ over a broad range of temperatures, from 10 to 300 K. We observed neither mode softening nor any other spectroscopic signature of lattice instabilities

  18. Utilization of evolutionary model, bioinformatics and heuristics for development of a multiplex Escherichia coli O157:H7 PCR assay

    Science.gov (United States)

    Introduction: Escherichia coli O157:H7 is a devastating foodborne pathogen causing many foodborne outbreaks worldwide with significant morbidity and mortality. The plasticity of the E. coli O157:H7 genome, inconsistent expression of surface antigens, and sharing of genetic elements with other non-...

  19. Characterization, Genome Sequence, and Analysis of Escherichia Phage CICC 80001, a Bacteriophage Infecting an Efficient L-Aspartic Acid Producing Escherichia coli.

    Science.gov (United States)

    Xu, Youqiang; Ma, Yuyue; Yao, Su; Jiang, Zengyan; Pei, Jiangsen; Cheng, Chi

    2016-03-01

    Escherichia phage CICC 80001 was isolated from the bacteriophage contaminated medium of an Escherichia coli strain HY-05C (CICC 11022S) which could produce L-aspartic acid. The phage had a head diameter of 45-50 nm and a tail of about 10 nm. The one-step growth curve showed a latent period of 10 min and a rise period of about 20 min. The average burst size was about 198 phage particles per infected cell. Tests were conducted on the plaques, multiplicity of infection, and host range. The genome of CICC 80001 was sequenced with a length of 38,810 bp, and annotated. The key proteins leading to host-cell lysis were phylogenetically analyzed. One protein belonged to class II holin, and the other two belonged to the endopeptidase family and N-acetylmuramoyl-L-alanine amidase family, respectively. The genome showed the sequence identity of 82.7% with that of Enterobacteria phage T7, and carried ten unique open reading frames. The bacteriophage resistant E. coli strain designated CICC 11021S was breeding and its L-aspartase activity was 84.4% of that of CICC 11022S.

  20. 7 T renal MRI: challenges and promises.

    Science.gov (United States)

    de Boer, Anneloes; Hoogduin, Johannes M; Blankestijn, Peter J; Li, Xiufeng; Luijten, Peter R; Metzger, Gregory J; Raaijmakers, Alexander J E; Umutlu, Lale; Visser, Fredy; Leiner, Tim

    2016-06-01

    The progression to 7 Tesla (7 T) magnetic resonance imaging (MRI) yields promises of substantial increase in signal-to-noise (SNR) ratio. This increase can be traded off to increase image spatial resolution or to decrease acquisition time. However, renal 7 T MRI remains challenging due to inhomogeneity of the radiofrequency field and due to specific absorption rate (SAR) constraints. A number of studies has been published in the field of renal 7 T imaging. While the focus initially was on anatomic imaging and renal MR angiography, later studies have explored renal functional imaging. Although anatomic imaging remains somewhat limited by inhomogeneous excitation and SAR constraints, functional imaging results are promising. The increased SNR at 7 T has been particularly advantageous for blood oxygen level-dependent and arterial spin labelling MRI, as well as sodium MR imaging, thanks to changes in field-strength-dependent magnetic properties. Here, we provide an overview of the currently available literature on renal 7 T MRI. In addition, we provide a brief overview of challenges and opportunities in renal 7 T MR imaging.

  1. Generalized hedgehog ansatz and Gribov copies in regions with nontrivial topologies

    Science.gov (United States)

    Canfora, Fabrizio; Salgado-Rebolledo, Patricio

    2013-02-01

    In this paper the arising of Gribov copies both in Landau and Coulomb gauges in regions with nontrivial topologies but flat metric, (such as closed tubes S1×D2, or R×T2) will be analyzed. Using a novel generalization of the hedgehog ansatz beyond spherical symmetry, analytic examples of Gribov copies of the vacuum will be constructed. Using such ansatz, we will also construct the elliptic Gribov pendulum. The requirement of absence of Gribov copies of the vacuum satisfying the strong boundary conditions implies geometrical constraints on the shapes and sizes of the regions with nontrivial topologies.

  2. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

    NARCIS (Netherlands)

    Armour, J.A.; Palla, R.; Zeeuwen, P.L.J.M.; Heijer, M. den; Schalkwijk, J.; Hollox, E.J.

    2007-01-01

    Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and

  3. High-Performance, Multi-Node File Copies and Checksums for Clustered File Systems

    Science.gov (United States)

    Kolano, Paul Z.; Ciotti, Robert B.

    2012-01-01

    Modern parallel file systems achieve high performance using a variety of techniques, such as striping files across multiple disks to increase aggregate I/O bandwidth and spreading disks across multiple servers to increase aggregate interconnect bandwidth. To achieve peak performance from such systems, it is typically necessary to utilize multiple concurrent readers/writers from multiple systems to overcome various singlesystem limitations, such as number of processors and network bandwidth. The standard cp and md5sum tools of GNU coreutils found on every modern Unix/Linux system, however, utilize a single execution thread on a single CPU core of a single system, and hence cannot take full advantage of the increased performance of clustered file systems. Mcp and msum are drop-in replacements for the standard cp and md5sum programs that utilize multiple types of parallelism and other optimizations to achieve maximum copy and checksum performance on clustered file systems. Multi-threading is used to ensure that nodes are kept as busy as possible. Read/write parallelism allows individual operations of a single copy to be overlapped using asynchronous I/O. Multinode cooperation allows different nodes to take part in the same copy/checksum. Split-file processing allows multiple threads to operate concurrently on the same file. Finally, hash trees allow inherently serial checksums to be performed in parallel. Mcp and msum provide significant performance improvements over standard cp and md5sum using multiple types of parallelism and other optimizations. The total speed-ups from all improvements are significant. Mcp improves cp performance over 27x, msum improves md5sum performance almost 19x, and the combination of mcp and msum improves verified copies via cp and md5sum by almost 22x. These improvements come in the form of drop-in replacements for cp and md5sum, so are easily used and are available for download as open source software at http://mutil.sourceforge.net.

  4. Feasibility of high-resolution pituitary MRI at 7.0 tesla

    International Nuclear Information System (INIS)

    Rotte, Alexandra A.J. de; Kolk, Anja G. van der; Rutgers, Dik; Luijten, Peter R.; Hendrikse, Jeroen; Zelissen, Pierre M.J.; Visser, Fredy

    2014-01-01

    Since the pituitary gland measures 3-8 mm, imaging with the highest possible spatial resolution is important for the detection of even smaller lesions such as those seen in Cushing's disease. In the current feasibility study, we tested a multi-sequence MRI protocol to visualize the pituitary gland in high resolution at 7.0 Tesla (7.0 T). Ten healthy volunteers were examined with a 7.0 T pituitary gland protocol. The protocol consisted of a T1-weighted magnetization-prepared inversion recovery (MPIR) turbo spin-echo (TSE) sequence and a T2-weighted TSE sequence. Additionally, this protocol was tested in five patients with clinical and biochemical suspicion of a microadenoma. The dedicated protocol was successful in visualizing normal pituitary anatomy. At 7.0 T compared to 1.5 T, four times as many slices covered the pituitary gland in sagittal and coronal direction. In three patients, a lesion was diagnosed at 7.0 T, and was confirmed by histopathology to be a microadenoma. Head-to-head comparisons of 7.0 T with 1.5 T and 3.0 T are needed with larger samples of patients and with imaging times feasible for clinical settings. However, the current study suggests that high-resolution 7.0 T MRI of the pituitary gland may provide new perspectives when used as a second-line diagnostic examination in the specific context of Cushing's disease. (orig.)

  5. Feasibility of high-resolution pituitary MRI at 7.0 tesla

    Energy Technology Data Exchange (ETDEWEB)

    Rotte, Alexandra A.J. de; Kolk, Anja G. van der; Rutgers, Dik; Luijten, Peter R.; Hendrikse, Jeroen [University Medical Center Utrecht, Department of Radiology, Heidelberglaan 100, Postbox 85500, Utrecht (Netherlands); Zelissen, Pierre M.J. [University Medical Center Utrecht, Department of Internal Medicine (Section of Endocrinology), Utrecht (Netherlands); Visser, Fredy [University Medical Center Utrecht, Department of Radiology, Heidelberglaan 100, Postbox 85500, Utrecht (Netherlands); Philips Healthcare, Best (Netherlands)

    2014-08-15

    Since the pituitary gland measures 3-8 mm, imaging with the highest possible spatial resolution is important for the detection of even smaller lesions such as those seen in Cushing's disease. In the current feasibility study, we tested a multi-sequence MRI protocol to visualize the pituitary gland in high resolution at 7.0 Tesla (7.0 T). Ten healthy volunteers were examined with a 7.0 T pituitary gland protocol. The protocol consisted of a T1-weighted magnetization-prepared inversion recovery (MPIR) turbo spin-echo (TSE) sequence and a T2-weighted TSE sequence. Additionally, this protocol was tested in five patients with clinical and biochemical suspicion of a microadenoma. The dedicated protocol was successful in visualizing normal pituitary anatomy. At 7.0 T compared to 1.5 T, four times as many slices covered the pituitary gland in sagittal and coronal direction. In three patients, a lesion was diagnosed at 7.0 T, and was confirmed by histopathology to be a microadenoma. Head-to-head comparisons of 7.0 T with 1.5 T and 3.0 T are needed with larger samples of patients and with imaging times feasible for clinical settings. However, the current study suggests that high-resolution 7.0 T MRI of the pituitary gland may provide new perspectives when used as a second-line diagnostic examination in the specific context of Cushing's disease. (orig.)

  6. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha; Hamdan, Samir; Richardson, Charles C.

    2010-01-01

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha

    2010-04-06

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Antibiotic resistance of Verotoxigenic Escherichia coli isolated from vegetables

    Directory of Open Access Journals (Sweden)

    mojtaba boniadian

    2017-01-01

    Full Text Available Introduction: Human gastrointestinal disease caused by verotoxigenic Escherichia coli has been diagnosed for recent decades. Escherichia coli O157:H7 is the most important serotype of verotoxigenic Escherichia coli that cause hemolytic uremic syndrome and hemorrhagic colitis in humans. This study was conducted to determine the occurrence of verotoxigenic E. coli and antibiotic resistance of the isolates from vegetables. Materials and methods: A total of 500 fresh vegetable samples were collected randomly from retail shops in Shahrekord, Iran. E. coli was isolated and identified using bacteriological and biochemical tests. PCR method was used to identify the rbfE, stx1, stx2 and eae genes. Also, antibiotic resistance of the isolates was determined by disk diffusion method. Results: The results represented that among 25 isolates possess virulence genes, 40, 12 and 4% of the isolates contained eaeA, STx2, and both genes, respectively. But none of them contained H7, STx1, and rfbE genes. The antibiotic resistance pattern demonstrated that the isolates were highly resistant to Gentamycin and cefotoxime. Discussion and conclusion: The results of this study showed that the presence of verotoxigenic E.coli in vegetables; and high resistance of the isolates to antibiotics could be hazardous for public health.

  9. Inhibition of Escherichia coli O157:H7 on stainless steel using Pseudomonas veronii biofilms.

    Science.gov (United States)

    Kim, Y; Kim, H; Beuchat, L R; Ryu, J-H

    2018-05-01

    We produced a Pseudomonas veronii biofilm on the surface of a stainless steel that is inhibitory to Escherichia coli O157:H7. Pseudomonas veronii strain KACC 81051BP, isolated from lettuce, readily formed biofilm on the surface of stainless steel coupons (SSCs) immersed in tryptic soy broth at 25°C. Cells showed significantly (P ≤ 0·05) enhanced tolerance to desiccation stress (43% relative humidity (RH)) and retained antimicrobial activity against E. coli O157:H7. The number of E. coli O157:H7 (control; 4·1 ± 0·1 log CFU per coupon) on sterile SSCs decreased to 2·7 ± 0·2 log CFU per coupon after exposure to 43% RH at 25°C for 48 h, while the population of E. coli O157:H7 (4·1 ± 0·0 log CFU per coupon) on SSCs containing P. veronii biofilm decreased to below the theoretical detection limit (1·5 log CFU per coupon) within 24 h. The antimicrobial biofilm produced on stainless steel may have application in preventing cross-contamination by E. coli O157:H7 on other abiotic surfaces in food-contact environments. The presence of Escherichia coli O157:H7 on environmental surfaces of food manufacturing, transportation and storage facilities is a significant food safety concern because it can result in cross-contamination of food products. In this study, we developed a Pseudomonas veronii biofilm on the surface of a stainless steel that inhibits the growth of E. coli O157:H7. Since P. veronii in biofilm resists desiccation, it provides persistent antimicrobial activity. Information presented here provides novel and practical insights to developing biological strategies to inactivate E. coli O157:H7 on diverse surfaces in food processing and handling environments. © 2018 The Society for Applied Microbiology.

  10. Clinical application of bilateral high temporal and spatial resolution dynamic contrast-enhanced magnetic resonance imaging of the breast at 7 T

    Energy Technology Data Exchange (ETDEWEB)

    Pinker, K.; Baltzer, P.; Bernathova, M.; Weber, M.; Leithner, D.; Helbich, T.H. [Medical University Vienna, Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Waehringer Guertel 18-20, 1090, Vienna (Austria); Bogner, W.; Trattnig, S.; Gruber, S.; Zaric, O. [Medical University Vienna, Department of Biomedical Imaging and Image-guided Therapy, MR Centre of Excellence, Vienna (Austria); Abeyakoon, O. [King' s College, Department of Radiology, London (United Kingdom); Dubsky, P. [Medical University Vienna, Department of Surgery, Vienna (Austria); Bago-Horvath, Z. [Medical University Vienna, Department of Pathology, Vienna (Austria)

    2014-04-15

    The objective of our study was to evaluate the clinical application of bilateral high spatial and temporal resolution dynamic contrast-enhanced magnetic resonance imaging (HR DCE-MRI) of the breast at 7 T. Following institutional review board approval 23 patients with a breast lesion (BIRADS 0, 4-5) were included in our prospective study. All patients underwent bilateral HR DCE-MRI of the breast at 7 T (spatial resolution of 0.7 mm{sup 3} voxel size, temporal resolution of 14 s). Two experienced readers (r1, r2) and one less experienced reader (r3) independently assessed lesions according to BI-RADS registered. Image quality, lesion conspicuity and artefacts were graded from 1 to 5. Sensitivity, specificity and diagnostic accuracy were assessed using histopathology as the standard of reference. HR DCE-MRI at 7 T revealed 29 lesions in 23 patients (sensitivity 100 % (19/19); specificity of 90 % (9/10)) resulting in a diagnostic accuracy of 96.6 % (28/29) with an AUC of 0.95. Overall image quality was excellent in the majority of cases (27/29) and examinations were not hampered by artefacts. There was excellent inter-reader agreement for diagnosis and image quality parameters (κ = 0.89-1). Bilateral HR DCE-MRI of the breast at 7 T is feasible with excellent image quality in clinical practice and allows accurate breast cancer diagnosis. (orig.)

  11. Efficient production of mutant phytase (phyA-7) derived from Selenomonas ruminantium using recombinant Escherichia coli in pilot scale.

    Science.gov (United States)

    Chi-Wei Lan, John; Chang, Chih-Kai; Wu, Ho-Shing

    2014-09-01

    A mutant gene of rumen phytase (phyA-7) was cloned into pET23b(+) vector and expressed in the Escherichia coli BL21 under the control of the T7 promoter. The study of fermentation conditions includes the temperature impacts of mutant phytase expression, the effect of carbon supplements over induction stage, the inferences of acetic acid accumulation upon enzyme expression and the comparison of one-stage and two-stage operations in batch mode. The maximum value of phytase activity was reached 107.0 U mL(-1) at induction temperature of 30°C. Yeast extract supplement demonstrated a significant increase on both protein concentration and phytase activity. The acetic acid (2 g L(-1)) presented in the modified synthetic medium demonstrated a significant decrease on expressed phytase activity. A two-stage batch operation enhanced the level of phytase activity from 306 to 1204 U mL(-1) in the 20 L of fermentation scale. An overall 3.7-fold improvement in phytase yield (35,375.72-1,31,617.50 U g(-1) DCW) was achieved in the two-stage operation. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  12. Elevated Expression of GlpT and UhpT via FNR Activation Contributes to Increased Fosfomycin Susceptibility in Escherichia coli under Anaerobic Conditions

    Science.gov (United States)

    Kurabayashi, Kumiko; Tanimoto, Koichi; Fueki, Shinobu; Tomita, Haruyoshi

    2015-01-01

    Because a shortage of new antimicrobial agents is a critical issue at present, and with the spread of multidrug-resistant (MDR) pathogens, the use of fosfomycin to treat infections is being revisited as a “last-resort option.” This drug offers a particular benefit in that it is more effective against bacteria growing under oxygen-limited conditions, unlike other commonly used antimicrobials, such as fluoroquinolones and aminoglycosides. In this study, we showed that Escherichia coli strains, including enterohemorrhagic E. coli (EHEC), were more susceptible to fosfomycin when grown anaerobically than when grown aerobically, and we investigated how the activity of this drug was enhanced during anaerobic growth of E. coli. Our quantitative PCR analysis and a transport assay showed that E. coli cells grown under anaerobic conditions had higher levels of expression of glpT and uhpT, encoding proteins that transport fosfomycin into cells with their native substrates, i.e., glycerol-3-phosphate and glucose-6-phosphate, and led to increased intracellular accumulation of the drug. Elevation of expression of these genes during anaerobic growth requires FNR, a global transcriptional regulator that is activated under anaerobic conditions. Purified FNR bound to DNA fragments from regions upstream of glpT and uhpT, suggesting that it is an activator of expression of glpT and uhpT during anaerobic growth. We concluded that the increased antibacterial activity of fosfomycin toward E. coli under anaerobic conditions can be attributed to elevated expression of GlpT and UhpT following activation of FNR, leading to increased uptake of the drug. PMID:26248376

  13. Applying independent component analysis to clinical fMRI at 7 T

    OpenAIRE

    Simon Daniel Robinson; Veronika eSchöpf; Pedro eCardoso; Alexander eGeissler; Alexander eGeissler; Florian Ph.S Fischmeister; Florian Ph.S Fischmeister; Moritz eWurnig; Moritz eWurnig; Siegfried eTrattnig; Roland eBeisteiner; Roland eBeisteiner

    2013-01-01

    Increased BOLD sensitivity at 7 T offers the possibility to increase the reliability of fMRI, but ultra-high field is also associated with an increase in artifacts related to head motion, Nyquist ghosting and parallel imaging reconstruction errors. In this study, the ability of Independent Component Analysis (ICA) to separate activation from these artifacts was assessed in a 7 T study of neurological patients performing chin and hand motor tasks. ICA was able to isolate primary motor activati...

  14. Scaling up Copy Detection

    OpenAIRE

    Li, Xian; Dong, Xin Luna; Lyons, Kenneth B.; Meng, Weiyi; Srivastava, Divesh

    2015-01-01

    Recent research shows that copying is prevalent for Deep-Web data and considering copying can significantly improve truth finding from conflicting values. However, existing copy detection techniques do not scale for large sizes and numbers of data sources, so truth finding can be slowed down by one to two orders of magnitude compared with the corresponding techniques that do not consider copying. In this paper, we study {\\em how to improve scalability of copy detection on structured data}. Ou...

  15. Curli Fibers Are Highly Conserved between Salmonella typhimurium and Escherichia coli with Respect to Operon Structure and Regulation

    Science.gov (United States)

    Römling, Ute; Bian, Zhao; Hammar, Mårten; Sierralta, Walter D.; Normark, Staffan

    1998-01-01

    Mouse-virulent Salmonella typhimurium strains SR-11 and ATCC 14028-1s express curli fibers, thin aggregative fibers, at ambient temperature on plates as judged by Western blot analysis and electron microscopy. Concomitantly with curli expression, cells develop a rough and dry colony morphology and bind the dye Congo red (called the rdar morphotype). Cloning and characterization of the two divergently transcribed operons required for curli biogenesis, csgBA(C) and csgDEFG, from S. typhimurium SR-11 revealed the same gene order and flanking genes as in Escherichia coli. The divergence of the curli region between S. typhimurium and E. coli at the nucleotide level is above average (22.4%). However, a high level of conservation at the protein level, which ranged from 86% amino acid homology for the fiber subunit CsgA to 99% homology for the lipoprotein CsgG, implies functional constraints on the gene products. Consequently, S. typhimurium genes on low-copy-number plasmids were able to complement respective E. coli mutants, although not always to wild-type levels. rpoS and ompR are required for transcriptional activation of (at least) the csgD promoter. The high degree of conservation at the protein level and the identical regulation patterns in E. coli and S. typhimurium suggest similar roles of curli fibers in the same ecological niche in the two species. PMID:9457880

  16. Optimisation of T2*-weighted MRI for the detection of small veins in multiple sclerosis at 3 T and 7 T

    International Nuclear Information System (INIS)

    Dixon, Jennifer Elizabeth; Simpson, Ashley; Mistry, Niraj; Evangelou, Nikos; Morris, Peter Gordon

    2013-01-01

    T 2 * -weighted magnetic resonance imaging at 7 T has recently been shown to allow differentiation between white-matter multiple sclerosis lesions and asymptomatic white-matter lesions, by the presence or absence of a detectable central blood vessel. The aim of the present work is to improve the technique by increasing the sensitivity to veins at both 3 T and 7 T, and to assess the benefit of ultra-high-field imaging. Signal-to-noise ratio (SNR) measurements and simulations are used to compare the sensitivity of magnitude T 2 * -weighted and susceptibility-weighted images for the detection of small veins (<1 pixel in diameter), both with and without the use of gadolinium. The simulations are used to predict the optimal scanning parameters in order to increase the sensitivity to these veins at both field strengths, and to reduce the inherent dependence on vessel orientation. The sensitivities of the sequences at both field strengths are compared, theoretically and experimentally, in order to quantify the benefit of imaging at ultra-high-field. Subjects with multiple sclerosis (MS) are scanned at both field strengths, using the optimised sequence parameters, as well as those used in previously published work, and the optimisation is shown to improve the detection of veins within lesions

  17. Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA and HIV-1 nef Genes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Siti Aisyah Mualif

    Full Text Available Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef, HIV-1 p24 (ca, and HIV-1 vif in NiCo21(DE3 E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.

  18. Combined effect of ultrasound, heat, and pressure on Escherichia coli O157:H7, polyphenol oxidase activity, and anthocyanins in blueberry (Vaccinium corymbosum) juice.

    Science.gov (United States)

    Zhu, Jinyan; Wang, Yuehua; Li, Xinghe; Li, Bin; Liu, Suwen; Chang, Nan; Jie, Ding; Ning, Chong; Gao, Haiyan; Meng, Xianjun

    2017-07-01

    The objective of this study was to evaluate the effect of different treatments-heat treatment (HT), sonication (SC), thermosonication (TS), manosonication (MS), manothermal (MT), and manothermosonication (MTS) on Escherichia coli O157:H7, polyphenol oxidase (PPO), and anthocyanin content in blueberry juice. First, samples were treated at different temperatures (30, 40, 50, 60, 70, and 80°C) and power intensities (280, 420, 560, and 700W) for 10min. Subsequently, samples were treated using combinations of power intensity and mild temperature for 10min. For further study, samples were treated using HT (80°C), TS (40°C, 560W), MT (350MPa, 40°C), MS (560W, 5min/350MPa), or MTS (560W, 5min, 40°C/350MPa, 40°C) for 5, 10, 15, 20min for each treatment, and the results compared between treatments. HT significantly reduced PPO activation (2.05% residual activity after only 5min), and resulted in a 2.00-log reduction in E. coli O157:H7 and an 85.25% retention of anthocyanin. Escherichia coli O157:H7 was slightly inactivated by TS after 5min (0.17-log reduction), while residual PPO activity was 23.36% and anthocyanin retention was 98.48%. However, Escherichia coli O157:H7 was rapidly inactivated by MTS (5.85-log reduction) after 5min, while anthocyanin retention was 97.49% and residual PPO activity dropped to 10.91%. The destruction of E. coli cells as a result of these treatments were confirmed using SEM and TEM. Therefore, a combination of sonication, high pressure, and mild heat allows the safety of blueberry juice to be maintained without compromising the retention of desirable antioxidant compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. The Home Copying Loophole Widens: Sony & Others v . Easyinternetcafé

    OpenAIRE

    Free, Dominic; Garnett, Nic

    2003-01-01

    The record industry is engaged in a determined campaign to stop the unlawful copying of music files downloaded via the Internet. In Sony & Others v. Easyinternetcafé [2003] All ER(D) 249 proceedings were brought by several major record companies to prevent Easyinternetcafé from providing a service copying music files onto CDs for its customers. The claimants succeeded in their aim. However the summary judgment which they obtained had a sting in the tail. It supports the proposition that t...

  20. Effects of cattle feeding regimen and soil management type on the fate of Escherichia coli O157:H7 and salmonella enterica serovar typhimurium in manure, manure-amended soil, and lettuce

    NARCIS (Netherlands)

    Franz, Eelco; van Diepeningen, Anne D; de Vos, Oscar J; van Bruggen, Ariena H C

    2005-01-01

    Survival of the green fluorescent protein-transformed human pathogens Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium was studied in a laboratory-simulated lettuce production chain. Dairy cows were fed three different roughage types: high-digestible grass silage plus maize

  1. Effects of cattle feeding regimen and soil management type on the fate of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium in manure, manure-amended soil, and lettuce

    NARCIS (Netherlands)

    Franz, E.; Diepeningen, van A.D.; Vos, de O.J.; Bruggen, van A.H.C.

    2005-01-01

    Survival of the green fluorescent protein-transformed human pathogens Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium was studied in a laboratory-simulated lettuce production chain. Dairy cows were fed three different roughage types: high-digestible grass silage plus maize

  2. Escherichia coli O157:H7 induces stronger plant immunity than Salmonella enterica Typhimurium SL1344.

    Science.gov (United States)

    Roy, Debanjana; Panchal, Shweta; Rosa, Bruce A; Melotto, Maeli

    2013-04-01

    Consumption of fresh produce contaminated with bacterial human pathogens has resulted in various, sometimes deadly, disease outbreaks. In this study, we assessed plant defense responses induced by the fully pathogenic bacteria Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium SL1344 in both Arabidopsis thaliana and lettuce (Lactuca sativa). Unlike SL1344, O157:H7 induced strong plant immunity at both pre-invasion and post-invasion steps of infection. For instance, O157:H7 triggered stomatal closure even under high relative humidity, an environmental condition that generally weakens plant defenses against bacteria in the field and laboratory conditions. SL1344 instead induced a transient stomatal immunity. We also observed that PR1 gene expression was significantly higher in Arabidopsis leaves infected with O157:H7 compared with SL1344. These results suggest that plants may recognize and respond to some human pathogens more effectively than others. Furthermore, stomatal immunity can diminish the penetration of human pathogens through the leaf epidermis, resulting in low bacterial titers in the plant apoplast and suggesting that additional control measures can be employed to prevent food contamination. The understanding of how plant responses can diminish bacterial contamination is paramount in preventing outbreaks and improving the safety of food supplies.

  3. High-level expression of Bacillus naganoensis pullulanase from recombinant Escherichia coli with auto-induction: effect of lac operator.

    Directory of Open Access Journals (Sweden)

    Yao Nie

    Full Text Available Pullulanase plays an important role in specific hydrolysis of branch points in amylopectin and is generally employed as an important enzyme in starch-processing industry. So far, however, the production level of pullulanase is still somewhat low from wide-type strains and even heterologous expression systems. Here the gene encoding Bacillus naganoensis pullulanase was amplified and cloned. For expression of the protein, two recombinant systems, Escherichia coli BL21(DE3/pET-20b(+-pul and E. coli BL21(DE3/pET-22b(+-pul, were constructed, both bearing T7 promoter and signal peptide sequence, but different in the existance of lac operator and lacI gene encoding lac repressor. Recombinant pullulanase was initially expressed with the activity of up to 14 U/mL by E. coli BL21(DE3/pET-20b(+-pul with IPTG induction in LB medium, but its expression level reduced continually with the extension of cryopreservation time and basal expression was observed. However, E. coli BL21(DE3/pET-22b(+-pul , involving lac operator downstream of T7 promoter to regulate foreign gene transcription, exhibited pullulanase activity consistently without detected basal expression. By investigating the effect of lac operator, basal expression of foreign protein was found to cause expression instability and negative effect on production of target protein. Thus double-repression strategy was proposed that lac operators in both chromosome and plasmid were bound with lac repressor to repress T7 RNA polymerase synthesis and target protein expression before induction. Consequently, the total activity of pullulanase was remarkably increased to 580 U/mL with auto-induction by lac operator-involved E. coli BL21(DE3/pET-22b(+-pul. When adding 0.6% glycine in culture, the extracellular production of pullulanase was significantly improved with the extracellular activity of 502 U/mL, which is a relatively higher level achieved to date for extracellular production of pullulanase. The

  4. High T/sub c/ screen-printed YBa2Cu3O/sub 7-//sub x/ films: Effect of the substrate material

    International Nuclear Information System (INIS)

    Bansal, N.P.; Simons, R.N.; Farrell, D.E.

    1988-01-01

    Thick films of YBa 2 Cu 3 O/sub 7-//sub x/ have been deposited on highly polished alumina, magnesia spinel, nickel aluminum titanate (Ni-Al-Ti), and barium tetratitanate (Ba-Ti) substrates by the screen printing technique. They were baked at 1000 0 C for 15 min, oxygen annealed at a lower temperature, and characterized by electrical resistivity measurements, x-ray diffraction, and optical and scanning electron microscopy. Properties of the films were found to be highly sensitive to the choice of the substrate material. The film on Ba-Ti turned green after firing, due to a reaction with the substrate and were insulating. A film on Ni-Al-Ti had a T/sub c/ (onset) ∼95 K and lost 90% of its resistance by ∼75 K. However, even at 4 K it was not fully superconducting, possibly due to a reaction between the film and the substrate and interdiffusion of the reaction products. The film on alumina had T/sub c/ (onset) ∼96 K, T/sub c/ (zero) ∼66 K, and ΔT/sub c/ (10--90%) ∼10 K. Our best film was obtained on spinel and had T/sub c/ (onset) ∼94 K, zero resistance at 81 K, and a transition width (10--90%) of ∼7 K

  5. Simulating Escherichia coli O157:H7 transmission to assess effectiveness of interventions in Dutch dairy-beef slaughterhouses

    NARCIS (Netherlands)

    Vosough Ahmadi, B.; Velthuis, A.G.J.; Hogeveen, H.; Huirne, R.B.M.

    2006-01-01

    Beef contamination with Escherichia coli O157:H7 (VTEC) is an important food-safety issue. To investigate the effectiveness of interventions against VTEC in Dutch beef industrial slaughterhouses that slaughter 500 dairy cattle per day, a Monte Carlo simulation model was built. We examined seven

  6. IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study.

    Directory of Open Access Journals (Sweden)

    Yunlei Li

    2016-12-01

    Full Text Available Pediatric acute lymphoblastic leukemia (ALL is the most common childhood cancer and the leading cause of cancer-related mortality in children. T cell ALL (T-ALL represents about 15% of pediatric ALL cases and is considered a high-risk disease. T-ALL is often associated with resistance to treatment, including steroids, which are currently the cornerstone for treating ALL; moreover, initial steroid response strongly predicts survival and cure. However, the cellular mechanisms underlying steroid resistance in T-ALL patients are poorly understood. In this study, we combined various genomic datasets in order to identify candidate genetic mechanisms underlying steroid resistance in children undergoing T-ALL treatment.We performed whole genome sequencing on paired pre-treatment (diagnostic and post-treatment (remission samples from 13 patients, and targeted exome sequencing of pre-treatment samples from 69 additional T-ALL patients. We then integrated mutation data with copy number data for 151 mutated genes, and this integrated dataset was tested for associations of mutations with clinical outcomes and in vitro drug response. Our analysis revealed that mutations in JAK1 and KRAS, two genes encoding components of the interleukin 7 receptor (IL7R signaling pathway, were associated with steroid resistance and poor outcome. We then sequenced JAK1, KRAS, and other genes in this pathway, including IL7R, JAK3, NF1, NRAS, and AKT, in these 69 T-ALL patients and a further 77 T-ALL patients. We identified mutations in 32% (47/146 of patients, the majority of whom had a specific T-ALL subtype (early thymic progenitor ALL or TLX. Based on the outcomes of these patients and their prednisolone responsiveness measured in vitro, we then confirmed that these mutations were associated with both steroid resistance and poor outcome. To explore how these mutations in IL7R signaling pathway genes cause steroid resistance and subsequent poor outcome, we expressed wild

  7. IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study

    Science.gov (United States)

    Stubbs, Andrew P.; Vroegindeweij, Eric M.; Smits, Willem K.; van Marion, Ronald; Dinjens, Winand N. M.; Horstmann, Martin; Kuiper, Roland P.; Zaman, Guido J. R.; van der Spek, Peter J.; Pieters, Rob; Meijerink, Jules P. P.

    2016-01-01

    Background Pediatric acute lymphoblastic leukemia (ALL) is the most common childhood cancer and the leading cause of cancer-related mortality in children. T cell ALL (T-ALL) represents about 15% of pediatric ALL cases and is considered a high-risk disease. T-ALL is often associated with resistance to treatment, including steroids, which are currently the cornerstone for treating ALL; moreover, initial steroid response strongly predicts survival and cure. However, the cellular mechanisms underlying steroid resistance in T-ALL patients are poorly understood. In this study, we combined various genomic datasets in order to identify candidate genetic mechanisms underlying steroid resistance in children undergoing T-ALL treatment. Methods and Findings We performed whole genome sequencing on paired pre-treatment (diagnostic) and post-treatment (remission) samples from 13 patients, and targeted exome sequencing of pre-treatment samples from 69 additional T-ALL patients. We then integrated mutation data with copy number data for 151 mutated genes, and this integrated dataset was tested for associations of mutations with clinical outcomes and in vitro drug response. Our analysis revealed that mutations in JAK1 and KRAS, two genes encoding components of the interleukin 7 receptor (IL7R) signaling pathway, were associated with steroid resistance and poor outcome. We then sequenced JAK1, KRAS, and other genes in this pathway, including IL7R, JAK3, NF1, NRAS, and AKT, in these 69 T-ALL patients and a further 77 T-ALL patients. We identified mutations in 32% (47/146) of patients, the majority of whom had a specific T-ALL subtype (early thymic progenitor ALL or TLX). Based on the outcomes of these patients and their prednisolone responsiveness measured in vitro, we then confirmed that these mutations were associated with both steroid resistance and poor outcome. To explore how these mutations in IL7R signaling pathway genes cause steroid resistance and subsequent poor outcome, we

  8. Plant lesions promote the rapid multiplication of Escherichia coli O157:H7 on post-harvest lettuce

    Science.gov (United States)

    Several outbreaks of Escherichia coli O157:H7 (EcO157) infections have been associated with minimally processed leafy vegetables in the U.S. Harvesting and processing cause plant tissue damage. In order to assess the role of plant tissue damage in the contamination of leafy greens with EcO157, the e...

  9. Peptide ligands specific to the oxidized form of escherichia coli thioredoxin.

    Energy Technology Data Exchange (ETDEWEB)

    Scholle, M. D.; Banach, B. S.; Hamdan, S. M.; Richardson, C. C.; Kay, B. K.; Biosciences Division; Amunix, Inc.; Univ. of Illinois at Chicago; Harvard Medical School

    2008-11-01

    Thioredoxin (Trx) is a highly conserved redox protein involved in several essential cellular processes. In this study, our goal was to isolate peptide ligands to Escherichia coli Trx that mimic protein-protein interactions, specifically the T7 polymerase-Trx interaction. To do this, we subjected Trx to affinity selection against a panel of linear and cysteine-constrained peptides using M13 phage display. A novel cyclized conserved peptide sequence, with a motif of C(D/N/S/T/G)D(S/T)-hydrophobic-C-X-hydrophobic-P, was isolated to Trx. These peptides bound specifically to the E. coli Trx when compared to the human and spirulina homologs. An alanine substitution of the active site cysteines (CGPC) resulted in a significant loss of peptide binding affinity to the Cys-32 mutant. The peptides were also characterized in the context of Trx's role as a processivity factor of the T7 DNA polymerase (gp5). As the interaction between gp5 and Trx normally takes place under reducing conditions, which might interfere with the conformation of the disulfide-bridged peptides, we made use of a 22 residue deletion mutant of gp5 in the thioredoxin binding domain (gp5{Delta}22) that bypassed the requirements of reducing conditions to interact with Trx. A competition study revealed that the peptide selectively inhibits the interaction of gp5{Delta}22 with Trx, under oxidizing conditions, with an IC50 of {approx} 10 {micro}M.

  10. Applying independent component analysis to clinical FMRI at 7t

    OpenAIRE

    Robinson, Simon Daniel; Schöpf, Veronika; Cardoso, Pedro; Geissler, Alexander; Fischmeister, Florian P S; Wurnig, Moritz; Trattnig, Siegfried; Beisteiner, Roland

    2013-01-01

    Increased BOLD sensitivity at 7T offers the possibility to increase the reliability of fMRI, but ultra-high field is also associated with an increase in artifacts related to head motion, Nyquist ghosting, and parallel imaging reconstruction errors. In this study, the ability of independent component analysis (ICA) to separate activation from these artifacts was assessed in a 7T study of neurological patients performing chin and hand motor tasks. ICA was able to isolate primary motor activat...

  11. Aislamiento, caracterización y subtipificación de cepas de Escherichia coli O157:H7 a partir de productos cárnicos y leche Isolation, characterization and typing of Escherichia coli O157:H7 strains from beef products and milk

    Directory of Open Access Journals (Sweden)

    M. L. Roldán

    2007-06-01

    Full Text Available Escherichia coli productor de toxina Shiga (Stx (STEC O157:H7 es un patógeno asociado a enfermedades transmitidas por alimentos, fundamentalmente de origen animal. Se investigó la presencia de E. coli O157 en 250 muestras de carne picada y hamburguesas obtenidas de comercios de las ciudades de Santa Fe y Santo Tomé (Pcia. de Santa Fe y en 150 muestras de leche provenientes de tanques de enfriado de tambos de la región, utilizando enriquecimiento selectivo y separación inmunomagnética. A partir de 3 muestras de carne (1,2% se aislaron cepas E. coli O157:H7 stx2, eae, y ehxA positivas, que pudieron ser diferenciadas mediante electroforesis de campo pulsado, fagotipificación y genotipificación de stx. No se aislaron cepas STEC O157:H7 a partir de las muestras de leche. Estos hallazgos confirman la participación de los alimentos de origen animal en la epidemiología de las enfermedades producidas por E. coli O157:H7.Shiga toxin (Stx-producing Escherichia coli (STEC is an emergent pathogen associated with foodborne diseases, especially foodstuffs of animal origin. A total of 250 beef samples (ground beef and hamburgers obtained from retail outlets in Santa Fe and Santo Tomé cities, and 150 milk samples from bulk tank milk from dairy barns of the region were analyzed by selective enrichment and immunomagnetic separation. Escherichia coli O157:H7 stx2, eae and ehxA positive strains were isolated from three (1.2% beef samples. The strains could be differentiated by pulsed-field gel electrophoresis, phagetyping and genotyping of stx. The milk samples were negative for STEC O157. These findings confirm the role of food of animal origin in the epidemiology of E. coli O157:H7 - associated diseases.

  12. Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex.

    Science.gov (United States)

    Lee, David J; Busby, Stephen J W; Westblade, Lars F; Chait, Brian T

    2008-02-01

    Bacteria contain a single multisubunit RNA polymerase that is responsible for the synthesis of all RNA. Previous studies of the Escherichia coli K-12 laboratory strain identified a group of effector proteins that interact directly with RNA polymerase to modulate the efficiency of transcription initiation, elongation, or termination. Here we used a rapid affinity isolation technique to isolate RNA polymerase from the pathogenic Escherichia coli strain O157:H7 Sakai. We analyzed the RNA polymerase enzyme complex using mass spectrometry and identified associated proteins. Although E. coli O157:H7 Sakai contains more than 1,600 genes not present in the K-12 strain, many of which are predicted to be involved in transcription regulation, all of the identified proteins in this study were encoded on the "core" E. coli genome.

  13. Quantitative effects of cell internalization of two types of ultrasmall superparamagnetic iron oxide nanoparticles at 4.7 T and 7 T

    International Nuclear Information System (INIS)

    Brisset, J.C.; Desestret, V.; Chauveau, F.; Nighoghossian, N.; Berthezene, Y.; Wiart, M.; Marcellino, S.; Lagarde, F.; Devillard, E.; Nataf, S.

    2010-01-01

    MRI coupled with the intravenous injection of ultrasmall superparamagnetic particles of iron oxides (USPIOs) is a promising tool for the study of neuroinflammation. Quantification of the approximate number of magnetically labelled macrophages may provide an effective and efficient method for monitoring inflammatory cells. The purpose of the present study was to characterise the relaxation properties of macrophages labelled with two types of USPIOs, at 4.7 T and 7 T. USPIO-labelled bone-marrow-derived macrophage phantoms were compared with phantoms of free dispersed USPIOs with the same global iron concentration, using multi-parametric (T1, T2 and T2*) quantitative MRI. The same protocol was then evaluated in living mice after intracerebral injection of iron-labelled macrophages vs free iron oxide. A linear relationship was observed among R1, R2 and R2* values and iron concentration in vitro at 4.7 T and at 7 T. At a given field, T1 and T2 relaxivities of both types of USPIOs decreased following internalisation into macrophages, while T2* relaxivities increased. There was fair overall agreement between the theoretical number of injected cells and the number estimated from T2 quantification and in vitro calibration curves, supporting the validity of the present in vitro calibration curves for in vivo investigation. (orig.)

  14. 7T T-2*-weighted magnetic resonance imaging reveals cortical phase differences between early- and late-onset Alzheimer's disease

    NARCIS (Netherlands)

    van Rooden, S.; Doan, N.T.; Versluis, M.J.; Goos, J.D.C.; Webb, A.G.; Oleksik, A.M.; van der Flier, W.M.; Scheltens, P.; Barkhof, F.; Weverlinge-Rynsburger, A.W.E.; Blauw, G. J.; Reiber, J.H.C.; van Buchem, M.A.; Milles, J.; van der Grond, J.

    2015-01-01

    The aim of this study is to explore regional iron-related differences in the cerebral cortex, indicative of Alzheimer's disease pathology, between early- and late-onset Alzheimer's disease (EOAD, LOAD, respectively) patients using 7T magnetic resonance phase images. High-resolution T

  15. Protective effects of lactoferrin chimera and bovine lactoferrin in a mouse model of enterohaemorrhagic Escherichia coli O157:H7 infection

    NARCIS (Netherlands)

    Flores-Villaseñor, H.; Canizalez-Román, A.; Velazquez-Roman, J.; Nazmi, K.; Bolscher, J.G.M.; Leon-Sicairos, N.

    2012-01-01

    Mice orally infected with enterohaemorrhagic Escherichia coli (EHEC) O157:H7 were used to evaluate the activity of bovine lactoferrin (bLF) and the synthetic peptide LFchimera. Groups of BALB/c mice inoculated intragastrically with EHEC O157:H7 showed chronic intestinal infection with the pathogen

  16. Persistence of Escherichia coli O157:H7 and total Escherichia coli in feces and feedlot surface manure from cattle fed diets with or without corn or sorghum wet distillers grains with solubles

    Science.gov (United States)

    Feeding corn wet distillers grains with solubles (WDGS) to cattle can increase the load of Escherichia coli O157:H7 in feces and on hides, but the mechanisms are not fully understood. The objective of these experiments was to examine a role for the persistence of E. coli O157:H7 in the feces and fee...

  17. Brain extraction in partial volumes T2*@7T by using a quasi-anatomic segmentation with bias field correction.

    Science.gov (United States)

    Valente, João; Vieira, Pedro M; Couto, Carlos; Lima, Carlos S

    2018-02-01

    Poor brain extraction in Magnetic Resonance Imaging (MRI) has negative consequences in several types of brain post-extraction such as tissue segmentation and related statistical measures or pattern recognition algorithms. Current state of the art algorithms for brain extraction work on weighted T1 and T2, being not adequate for non-whole brain images such as the case of T2*FLASH@7T partial volumes. This paper proposes two new methods that work directly in T2*FLASH@7T partial volumes. The first is an improvement of the semi-automatic threshold-with-morphology approach adapted to incomplete volumes. The second method uses an improved version of a current implementation of the fuzzy c-means algorithm with bias correction for brain segmentation. Under high inhomogeneity conditions the performance of the first method degrades, requiring user intervention which is unacceptable. The second method performed well for all volumes, being entirely automatic. State of the art algorithms for brain extraction are mainly semi-automatic, requiring a correct initialization by the user and knowledge of the software. These methods can't deal with partial volumes and/or need information from atlas which is not available in T2*FLASH@7T. Also, combined volumes suffer from manipulations such as re-sampling which deteriorates significantly voxel intensity structures making segmentation tasks difficult. The proposed method can overcome all these difficulties, reaching good results for brain extraction using only T2*FLASH@7T volumes. The development of this work will lead to an improvement of automatic brain lesions segmentation in T2*FLASH@7T volumes, becoming more important when lesions such as cortical Multiple-Sclerosis need to be detected. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope.

    Science.gov (United States)

    Zhang, Xiaojuan; Yao, Zhixuan; Duan, Yanting; Zhang, Xiaomei; Shi, Jinsong; Xu, Zhenghong

    2018-01-11

    The specific recognition and binding of promoter and RNA polymerase is the first step of transcription initiation in bacteria and largely determines transcription activity. Therefore, direct analysis of the interaction between promoter and RNA polymerase in vitro may be a new strategy for promoter characterization, to avoid interference due to the cell's biophysical condition and other regulatory elements. In the present study, the specific interaction between T7 promoter and T7 RNA polymerase was studied as a model system using force spectroscopy based on atomic force microscope (AFM). The specific interaction between T7 promoter and T7 RNA polymerase was verified by control experiments, and the rupture force in this system was measured as 307.2 ± 6.7 pN. The binding between T7 promoter mutants with various promoter activities and T7 RNA polymerase was analyzed. Interaction information including rupture force, rupture distance and binding percentage were obtained in vitro , and reporter gene expression regulated by these promoters was also measured according to a traditional promoter activity characterization method in vivo Using correlation analysis, it was found that the promoter strength characterized by reporter gene expression was closely correlated with rupture force and the binding percentage by force spectroscopy. These results indicated that the analysis of the interaction between promoter and RNA polymerase using AFM-based force spectroscopy was an effective and valid approach for the quantitative characterization of promoters. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  19. Elucidating the pH-Dependent Structural Transition of T7 Bacteriophage Endolysin.

    Science.gov (United States)

    Sharma, Meenakshi; Kumar, Dinesh; Poluri, Krishna Mohan

    2016-08-23

    Bacteriophages are the most abundant and diverse biological entities on earth. Bacteriophage endolysins are unique peptidoglycan hydrolases and have huge potential as effective enzybiotics in various infectious models. T7 bacteriophage endolysin (T7L), also known as N-acetylmuramoyl-l-alanine amidase or T7 lysozyme, is a 17 kDa protein that lyses a range of Gram-negative bacteria by hydrolyzing the amide bond between N-acetylmuramoyl residues and the l-alanine of the peptidoglycan layer. Although the activity profiles of several of the T7 family members have been known for many years, the molecular basis for their pH-dependent differential activity is not clear. In this study, we explored the pH-induced structural, stability, and activity characteristics of T7L by applying a variety of biophysical techniques and protein nuclear magnetic resonance (NMR) spectroscopy. Our studies established a reversible structural transition of T7L below pH 6 and the formation of a partially denatured conformation at pH 3. This low-pH conformation is thermally stable and exposed its hydrophobic pockets. Further, NMR relaxation measurements and structural analysis unraveled that T7L is highly dynamic in its native state and a network of His residues are responsible for the observed pH-dependent conformational dynamics and transitions. As bacteriophage chimeric and engineered endolysins are being developed as novel therapeutics against multiple drug resistance pathogens, we believe that our results are of great help in designing these entities as broadband antimicrobial and/or antibacterial agents.

  20. Original Copies

    DEFF Research Database (Denmark)

    Sørensen, Tim Flohr

    2013-01-01

    of similarity by looking at artefactual similarity as the results of prototyping and as a production of simulacra. In this light, the concept of copying turns out to be more than simply a matter of trying to imitate an exotic or prestigious original, and it fundamentally raises the question how different a copy...

  1. Quantum copying: A review

    Directory of Open Access Journals (Sweden)

    Mark Hillery

    2000-07-01

    Full Text Available Quantum information is stored in two-level quantum systems known as qubits. The no-cloning theorem states that the state of an unknown qubit cannot be copied. This is in contrast to classical information which can be copied. If one drops the requirement that the copies be perfect it is possible to design quantum copiers. This paper presents a short review of the theory of quantum copying.

  2. 7 T renal MRI : challenges and promises

    NARCIS (Netherlands)

    de Boer, A.; Hoogduin, J.M.; Blankestijn, P.J.; Li, X.; Luijten, P.R.; Metzger, G.J.; Raaijmakers, A.J.E.; Umutlu, L.; Visser, F.; Leiner, T.

    The progression to 7 Tesla (7 T) magnetic resonance imaging (MRI) yields promises of substantial increase in signal-to-noise (SNR) ratio. This increase can be traded off to increase image spatial resolution or to decrease acquisition time. However, renal 7 T MRI remains challenging due to

  3. Mutational analysis of Escherichia coli elongation factor Tu in search of a role for the N-terminal region

    DEFF Research Database (Denmark)

    Mansilla, Francisco; Knudsen, Charlotte Rohde; Laurberg, M

    1998-01-01

    We have mutated lysine 2 and arginine 7 in elongation factor Tu from Escherichia coli separately either to alanine or glutamic acid. The aim of the work was to reveal the possible interactions between the conserved N-terminal part of the molecule, which is rich in basic residues and aminoacyl...... this activity. Furthermore, arginine 7 seems to play a role in regulating the binding of GTP. The three-dimensional structure of the ternary complex, EF-Tu:GTP:Phe-tRNAPhe, involving Thermus aquaticus EF-Tu and yeast Phe-tRNA(Phe), shows that Arg7 is in a position which permits salt bridge formation with Asp284...

  4. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.

    OpenAIRE

    Meier-Kolthoff, Jan P; Hahnke, Richard L; Petersen, Jörn; Scheuner, Carmen; Michael, Victoria; Fiebig, Anne; Rohde, Christine; Rohde, Manfred; Fartmann, Berthold; Goodwin, Lynne A; Chertkov, Olga; Reddy, Tbk; Pati, Amrita; Ivanova, Natalia N; Markowitz, Victor

    2014-01-01

    Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083T together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes ...

  5. Quantification of contamination of lettuce by GFP-expressing Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium

    NARCIS (Netherlands)

    Franz, Eelco; Visser, Anna A; Van Diepeningen, Anne D; Klerks, Michel M; Termorshuizen, Aad J; van Bruggen, Ariena H C

    The primary objective of this study was to determine the possibility of internalization of GFP-expressing Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium (S. Typhimurium) strains MAE 110 (multi-cellular morphology) and 119 (wild type morphology) into lettuce seedlings (Lactuca

  6. Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.

    Directory of Open Access Journals (Sweden)

    Verena Jabs

    Full Text Available Non-small cell lung cancer (NSCLC represents a genomically unstable cancer type with extensive copy number aberrations. The relationship of gene copy number alterations and subsequent mRNA levels has only fragmentarily been described. The aim of this study was to conduct a genome-wide analysis of gene copy number gains and corresponding gene expression levels in a clinically well annotated NSCLC patient cohort (n = 190 and their association with survival. While more than half of all analyzed gene copy number-gene expression pairs showed statistically significant correlations (10,296 of 18,756 genes, high correlations, with a correlation coefficient >0.7, were obtained only in a subset of 301 genes (1.6%, including KRAS, EGFR and MDM2. Higher correlation coefficients were associated with higher copy number and expression levels. Strong correlations were frequently based on few tumors with high copy number gains and correspondingly increased mRNA expression. Among the highly correlating genes, GO groups associated with posttranslational protein modifications were particularly frequent, including ubiquitination and neddylation. In a meta-analysis including 1,779 patients we found that survival associated genes were overrepresented among highly correlating genes (61 of the 301 highly correlating genes, FDR adjusted p<0.05. Among them are the chaperone CCT2, the core complex protein NUP107 and the ubiquitination and neddylation associated protein CAND1. In conclusion, in a comprehensive analysis we described a distinct set of highly correlating genes. These genes were found to be overrepresented among survival-associated genes based on gene expression in a large collection of publicly available datasets.

  7. Affinity Isolation and I-DIRT Mass Spectrometric Analysis of the Escherichia coli O157:H7 Sakai RNA Polymerase Complex▿

    Science.gov (United States)

    Lee, David J.; Busby, Stephen J. W.; Westblade, Lars F.; Chait, Brian T.

    2008-01-01

    Bacteria contain a single multisubunit RNA polymerase that is responsible for the synthesis of all RNA. Previous studies of the Escherichia coli K-12 laboratory strain identified a group of effector proteins that interact directly with RNA polymerase to modulate the efficiency of transcription initiation, elongation, or termination. Here we used a rapid affinity isolation technique to isolate RNA polymerase from the pathogenic Escherichia coli strain O157:H7 Sakai. We analyzed the RNA polymerase enzyme complex using mass spectrometry and identified associated proteins. Although E. coli O157:H7 Sakai contains more than 1,600 genes not present in the K-12 strain, many of which are predicted to be involved in transcription regulation, all of the identified proteins in this study were encoded on the “core” E. coli genome. PMID:18083804

  8. Galectin-1 as a fusion partner for the production of soluble and folded human {beta}-1,4-galactosyltransferase-T7 in E. coli

    Energy Technology Data Exchange (ETDEWEB)

    Pasek, Marta [Structural Glycobiology Section, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 2170 (United States); Boeggeman, Elizabeth; Ramakrishnan, Boopathy [Structural Glycobiology Section, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 2170 (United States); Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 2170 (United States); Qasba, Pradman K., E-mail: qasba@helix.nih.gov [Structural Glycobiology Section, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 2170 (United States)

    2010-04-09

    The expression of recombinant proteins in Escherichia coli often leads to inactive aggregated proteins known as the inclusion bodies. To date, the best available tool has been the use of fusion tags, including the carbohydrate-binding protein; e.g., the maltose-binding protein (MBP) that enhances the solubility of recombinant proteins. However, none of these fusion tags work universally with every partner protein. We hypothesized that galectins, which are also carbohydrate-binding proteins, may help as fusion partners in folding the mammalian proteins in E. coli. Here we show for the first time that a small soluble lectin, human galectin-1, one member of a large galectin family, can function as a fusion partner to produce soluble folded recombinant human glycosyltransferase, {beta}-1,4-galactosyltransferase-7 ({beta}4Gal-T7), in E. coli. The enzyme {beta}4Gal-T7 transfers galactose to xylose during the synthesis of the tetrasaccharide linker sequence attached to a Ser residue of proteoglycans. Without a fusion partner, {beta}4Gal-T7 is expressed in E. coli as inclusion bodies. We have designed a new vector construct, pLgals1, from pET-23a that includes the sequence for human galectin-1, followed by the Tev protease cleavage site, a 6x His-coding sequence, and a multi-cloning site where a cloned gene is inserted. After lactose affinity column purification of galectin-1-{beta}4Gal-T7 fusion protein, the unique protease cleavage site allows the protein {beta}4Gal-T7 to be cleaved from galectin-1 that binds and elutes from UDP-agarose column. The eluted protein is enzymatically active, and shows CD spectra comparable to the folded {beta}4Gal-T1. The engineered galectin-1 vector could prove to be a valuable tool for expressing other proteins in E. coli.

  9. Most probable number methodology for quantifying dilute concentrations and fluxes of Escherichia coli O157:H7 in surface waters.

    Science.gov (United States)

    Jenkins, M B; Endale, D M; Fisher, D S; Gay, P A

    2009-02-01

    To better understand the transport and enumeration of dilute densities of Escherichia coli O157:H7 in agricultural watersheds, we developed a culture-based, five tube-multiple dilution most probable number (MPN) method. The MPN method combined a filtration technique for large volumes of surface water with standard selective media, biochemical and immunological tests, and a TaqMan confirmation step. This method determined E. coli O157:H7 concentrations as low as 0.1 MPN per litre, with a 95% confidence level of 0.01-0.7 MPN per litre. Escherichia coli O157:H7 densities ranged from not detectable to 9 MPN per litre for pond inflow, from not detectable to 0.9 MPN per litre for pond outflow and from not detectable to 8.3 MPN per litre for within pond. The MPN methodology was extended to mass flux determinations. Fluxes of E. coli O157:H7 ranged from 10(4) MPN per hour. This culture-based method can detect small numbers of viable/culturable E. coli O157:H7 in surface waters of watersheds containing animal agriculture and wildlife. This MPN method will improve our understanding of the transport and fate of E. coli O157:H7 in agricultural watersheds, and can be the basis of collections of environmental E. coli O157:H7.

  10. Pathogenesis of Escherichia coli O157:H7 Strain 86-24 Following Oral Infection of BALB/c Mice with an Intact Commensal Flora

    Science.gov (United States)

    2010-01-01

    inocula of these organisms are also needed to achieve colonization and disease in monkeys [29] and rabbits [30]. Our data suggested that the predominate...SB. Escherichia coli 0157:H7 srrains associared wirh haemorrhagic colitis in rhe Unired Srares produce a Shigella dysenreriae 1 (SHIGA) like...611-20. (29) Kang G, Pulimood AB, Koshi R. Hull A, Acheson D. Rajan P. er al. A monkey model for enrerohemorrhagic Escherichia coli infection. j

  11. Complete mitochondrial genome of endangered Yellow-shouldered Amazon (Amazona barbadensis): two control region copies in parrot species of the Amazona genus.

    Science.gov (United States)

    Urantowka, Adam Dawid; Hajduk, Kacper; Kosowska, Barbara

    2013-08-01

    Amazona barbadensis is an endangered species of parrot living in northern coastal Venezuela and in several Caribbean islands. In this study, we sequenced full mitochondrial genome of the considered species. The total length of the mitogenome was 18,983 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, duplicated control region, and degenerate copies of ND6 and tRNA (Glu) genes. High degree of identity between two copies of control region suggests their coincident evolution and functionality. Comparative analysis of both the control region sequences from four Amazona species revealed their 89.1% identity over a region of 1300 bp and indicates the presence of distinctive parts of two control region copies.

  12. Influence of culture conditions on Escherichia coli O157:H7 biofilm formation by atomic force microscopy

    International Nuclear Information System (INIS)

    Oh, Y.J.; Jo, W.; Yang, Y.; Park, S.

    2007-01-01

    Biofilms are complex microbial communities that are resistant against attacks by bacteriophages and removal by drugs and chemicals. In this study, biofilms of Escherichia coli O157:H7, a bacterial pathogen, were investigated using atomic force microscopy (AFM) in terms of the dynamic transition of morphology and surface properties of bacterial cells over the development of biofilms. The physical and topographical properties of biofilms are different, depending on nutrient availability. Compared to biofilms formed in a high nutrient medium, biofilms form faster and a higher number of bacterial cells were recovered on glass surface in a low nutrient medium. We demonstrate that AFM can obtain high-resolution images and the elastic information about biofilms. As E. coli biofilm becomes mature, the magnitude of the force between a tip and the surface of the biofilm gets stronger, suggesting that extracellular polymeric substances (EPSs), sticky components of biofilms, accumulate over the surface of cells upon the initial attachment of bacterial cells to surfaces

  13. Multi-turn multi-gap transmission line resonators - Concept, design and first implementation at 4.7T and 7T.

    Science.gov (United States)

    Frass-Kriegl, Roberta; Laistler, Elmar; Hosseinnezhadian, Sajad; Schmid, Albrecht Ingo; Moser, Ewald; Poirier-Quinot, Marie; Darrasse, Luc; Ginefri, Jean-Christophe

    2016-12-01

    A novel design scheme for monolithic transmission line resonators (TLRs) is presented - the multi-turn multi-gap TLR (MTMG-TLR) design. The MTMG-TLR design enables the construction of TLRs with multiple turns and multiple gaps. This presents an additional degree of freedom in tuning self-resonant TLRs, as their resonance frequency is fully determined by the coil geometry (e.g. diameter, number of turns, conductor width, etc.). The novel design is evaluated at 4.7T and 7T by simulations and experiments, where it is demonstrated that MTMG-TLRs can be used for MRI, and that the B 1 distribution of MTMG-TLRs strongly depends on the number and distribution of turns. A comparison to conventional loop coils revealed that the B 1 performance of MTMG-TLRs is comparable to a loop coil with the same mean diameter; however, lower 10g SAR values were found for MTMG-TLRs. The MTMG-TLR design is expected to bring most benefits at high static field, where it allows for independent size and frequency selection, which cannot be achieved with standard TLR design. However, it also enables more accurate geometric optimization at low static field. Thereby, the MTMG-TLR design preserves the intrinsic advantages of TLRs, i.e. mechanical flexibility, high SAR efficiency, mass production, and coil miniaturization. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Optimisation of T{sub 2}{sup *}-weighted MRI for the detection of small veins in multiple sclerosis at 3 T and 7 T

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, Jennifer Elizabeth, E-mail: jennifer.dixon@nottingham.ac.uk [Sir Peter Mansfield Magnetic Resonance Centre, University of Nottingham, Nottingham, NG7 2RD (United Kingdom); Simpson, Ashley, E-mail: ashley.simpson@nhs.net [Academic Division of Clinical Neurology, University of Nottingham, Queen' s Medical Centre, Nottingham, NG7 2UH (United Kingdom); Mistry, Niraj, E-mail: niraj.mistry@nottingham.ac.uk [Academic Division of Clinical Neurology, University of Nottingham, Queen' s Medical Centre, Nottingham, NG7 2UH (United Kingdom); Evangelou, Nikos, E-mail: nikos.evangelou@nuh.nhs.uk [Academic Division of Clinical Neurology, University of Nottingham, Queen' s Medical Centre, Nottingham, NG7 2UH (United Kingdom); Morris, Peter Gordon, E-mail: peter.morris@nottingham.ac.uk [Sir Peter Mansfield Magnetic Resonance Centre, University of Nottingham, Nottingham, NG7 2RD (United Kingdom)

    2013-05-15

    T{sub 2}{sup *}-weighted magnetic resonance imaging at 7 T has recently been shown to allow differentiation between white-matter multiple sclerosis lesions and asymptomatic white-matter lesions, by the presence or absence of a detectable central blood vessel. The aim of the present work is to improve the technique by increasing the sensitivity to veins at both 3 T and 7 T, and to assess the benefit of ultra-high-field imaging. Signal-to-noise ratio (SNR) measurements and simulations are used to compare the sensitivity of magnitude T{sub 2}{sup *}-weighted and susceptibility-weighted images for the detection of small veins (<1 pixel in diameter), both with and without the use of gadolinium. The simulations are used to predict the optimal scanning parameters in order to increase the sensitivity to these veins at both field strengths, and to reduce the inherent dependence on vessel orientation. The sensitivities of the sequences at both field strengths are compared, theoretically and experimentally, in order to quantify the benefit of imaging at ultra-high-field. Subjects with multiple sclerosis (MS) are scanned at both field strengths, using the optimised sequence parameters, as well as those used in previously published work, and the optimisation is shown to improve the detection of veins within lesions.

  15. Antibacterial effect of lactoferricin B on Escherichia coli O157:H7 in ground beef.

    Science.gov (United States)

    Venkitanarayanan, K S; Zhao, T; Doyle, M P

    1999-07-01

    The antibacterial activity of lactoferricin B on enterohemorrhagic Escherichia coli O157:H7 in 1% peptone medium and ground beef was studied at 4 and 10 degrees C. In 1% peptone medium, 50 and 100 microg of lactoferricin B per ml reduced E. coli O157:H7 populations by approximately 0.7 and 2.0 log CFU/ml, respectively. Studies comparing the antibacterial effect of lactoferricin B on E. coli O157:H7 in 1% peptone at pH 5.5 and 7.2 did not reveal any significant difference (P > 0.5) at the two pH values. Lactoferricin B (100 microg/g) reduced E. coli O157:H7 population in ground beef by about 0.8 log CFU/g (P 0.5) was observed in the total plate count between treatment and control ground beef samples stored at 4 and 10 degrees C. The antibacterial effect of lactoferricin B on E. coli O157:H7 observed in this study is not of sufficient magnitude to merit its use in ground beef for controlling the pathogen.

  16. Assessment of Escherichia coli O157:H7 transference from soil to Iceberg Lettuce via a contaminated harvesting knife

    Science.gov (United States)

    The potential for coring knives to cross-contaminate lettuce heads with pathogens was evaluated for both ring and blade ends. Rings and blades artificially contaminated with Escherichia coli O157:H7 (EHEC), were used to core three successive heads of iceberg lettuce. The coring rings and blades were...

  17. Improved Design and Ultrasound-assisted Sanitation of Lettuce Harvesting Knives for Minimizing Escherichia coli O157:H7 Contamination

    Science.gov (United States)

    Laboratory studies have shown that Escherichia coli O157:H7 can be transferred to lettuce during harvesting. Knives used for lettuce coring-in-field (CIF) harvesting are likely to contact soil and consequently could serve as a vehicle for the transmission of food-borne human pathogens from contamin...

  18. 7T: Physics, safety, and potential clinical applications.

    Science.gov (United States)

    Kraff, Oliver; Quick, Harald H

    2017-12-01

    With more than 60 installed magnetic resonance imaging (MRI) systems worldwide operating at a magnetic field strength of 7T or higher, ultrahigh-field (UHF) MRI has been established as a platform for clinically oriented research in recent years. Profound technical and methodological developments have helped overcome the inherent physical challenges of UHF radiofrequency (RF) signal homogenization in the human body. The ongoing development of dedicated RF coil arrays was pivotal in realizing UHF body MRI, beyond mere brain imaging applications. Another precondition to clinical application of 7T MRI is the safety testing of implants and the establishment of safety concepts. Against this backdrop, 7T MRI and MR spectroscopy (MRS) recently have demonstrated capabilities and potentials for clinical diagnostics in a variety of studies. This article provides an overview of the immanent physical challenges of 7T UHF MRI and discusses recent technical solutions and safety concepts. Furthermore, recent clinically oriented studies are highlighted that span a broad application spectrum from 7T UHF brain to body MRI. 4 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2017;46:1573-1589. © 2017 International Society for Magnetic Resonance in Medicine.

  19. Genes for 7S RNAs can replace the gene for 4.5S RNA in growth of Escherichia coli

    DEFF Research Database (Denmark)

    Brown, S

    1991-01-01

    4.5S RNAs of eubacteria and 7S RNAs of archaebacteria and eukaryotes exist in a hairpin conformation. The apex of this hairpin displays structural and sequence similarities among both 4.5S and 7S RNAs. Furthermore, a hyphenated sequence of 16 nucleotides is conserved in all eubacterial 4.5S RNAs...... examined. In this article I report that 7S RNAs that contain this 16-nucleotide sequence are able to replace 4.5S RNAs and permit growth of Escherichia coli....

  20. Survival of Listeria monocytogenes, Yersinia enterocolitica and Escherichia coli O157:H7 and quality changes after irradiation of beef steaks and ground beef

    International Nuclear Information System (INIS)

    Fu, A.H.; Sebranek, J.G.; Murano, E.A.

    1995-01-01

    Beef steaks and ground beef were inoculated with Listeria monocytogenes, Yersinia enterocolitica, or Escherichia coli O157:H7. Samples were packaged in air or under vacuum and irradiated at low (0.60 to 0.80 kGy) or medium (1.5 to 2.0 kGy) doses, with each dose delivered at either a low (2.8 M/min conveyor speed) or high (6.9 M/min) dose rate. Medium-dose irradiation accompanied by 7 degrees C storage resulted in no Y. enterocolitica or E. coli O157:H7 survivors being detected. There was no effect on survival of the pathogens by dose rate or storage atmosphere. No difference (P0.05) was observed in meat pH or color, but TBA values increased after 7 days storage

  1. High throughput screening of human subtelomeric DNA for copy number changes using multiplex amplifiable probe hybridisation (MAPH).

    Science.gov (United States)

    Hollox, E J; Atia, T; Cross, G; Parkin, T; Armour, J A L

    2002-11-01

    Subtelomeric regions of the human genome are gene rich, with a high level of sequence polymorphism. A number of clinical conditions, including learning disability, have been attributed to subtelomeric deletions or duplications, but screening for deletion in these regions using conventional cytogenetic methods and fluorescence in situ hybridisation (FISH) is laborious. Here we report that a new method, multiplex amplifiable probe hybridisation (MAPH), can be used to screen for copy number at subtelomeric regions. We have constructed a set of MAPH probes with each subtelomeric region represented at least once, so that one gel lane can assay copy number at all chromosome ends in one person. Each probe has been sequenced and, where possible, its position relative to the telomere determined by comparison with mapped clones. The sensitivity of the probes has been characterised on a series of cytogenetically verified positive controls and 83 normal controls were used to assess the frequency of polymorphic copy number with no apparent phenotypic effect. We have also used MAPH to test a cohort of 37 people selected from males referred for fragile X syndrome testing and found six changes that were confirmed by dosage PCR. MAPH can be used to screen subtelomeric regions of chromosomes for deletions and duplications before confirmation by FISH or dosage PCR. The high throughput nature of this technique allows it to be used for large scale screening of subtelomeric copy number, before confirmation by FISH. In practice, the availability of a rapid and efficient screen may allow subtelomeric analysis to be applied to a wider selection of patients than is currently possible using FISH alone.

  2. Inhibition of IGF1-R overcomes IGFBP7-induced chemotherapy resistance in T-ALL

    International Nuclear Information System (INIS)

    Bartram, Isabelle; Erben, Ulrike; Ortiz-Tanchez, Jutta; Blunert, Katja; Schlee, Cornelia; Neumann, Martin; Heesch, Sandra; Baldus, Claudia D.

    2015-01-01

    T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease with the need for treatment optimization. Previously, high expression of Insulin-like growth factor binding protein 7 (IGFBP7), a member of the IGF system, was identified as negative prognostic factor in adult T-ALL patients. Since aberrant IGFBP7 expression was observed in a variety of neoplasia and was relevant for prognosis in T-ALL, we investigated the functional role of IGFBP7 in Jurkat and Molt-4 cells as in vitro models for T-ALL. Jurkat and Molt-4 cells were stably transfected with an IGFBP7 over-expression vector or the empty vector as control. Proliferation of the cells was assessed by WST-1 assays and cell cycle status was measured by flow-cytometry after BrDU/7-AAD staining. The effect of IGFBP7 over-expression on sensitivity to cytostatic drugs was determined in AnnexinV/7-AAD assays. IGF1-R protein expression was measured by Western Blot and flow-cytometric analysis. IGF1-R associated gene expression profiles were generated from microarray gene expression data of 86 T-ALL patients from the Microarrays Innovations in Leukemia (MILE) multicenter study. IGFBP7-transfected Jurkat cells proliferated less, leading to a longer survival in a nutrient–limited environment. Both IGFBP7-transfected Jurkat and Molt-4 cells showed an arrest in the G0/G1 cell cycle phase. Furthermore, Jurkat IGFBP7-transfected cells were resistant to vincristine and asparaginase treatment. Surface expression and whole protein measurement of IGF1-R protein expression showed a reduced abundance of the receptor after IGFBP7 transfection in Jurkat cells. Interestingly, combination of the IGF1-R inhibitor NPV-AEW541 restored sensitivity to vincristine in IGFBP7-transfected cells. Additionally, IGF1-R associated GEP revealed an up-regulation of important drivers of T-ALL pathogenesis and regulators of chemo-resistance and apoptosis such as NOTCH1, BCL-2, PRKCI, and TP53. This study revealed a

  3. Fate of naturally occurring Escherichia coli O157:H7 and other zoonotic pathogens during minimally managed bovine feedlot manure composting processes

    Science.gov (United States)

    Reducing Escherichia coli O157:H7 in livestock manures before application to cropland is critical for reducing the risk of foodborne illness associated with produce. Our objective was to determine the fate of naturally occurring E. coli O157:H7 and other pathogens during minimally managed on-farm bo...

  4. Elimination of Pathogen Escherichia coli O157:H7 in Ground Beef by a Newly Isolated Strain of Lactobacillus acidophilus during Storage at 5°C

    Directory of Open Access Journals (Sweden)

    Alireza Goodarzi

    2016-06-01

    Full Text Available Background and Objective: Constant use of limited number of lactic acid bacteria species in biopreservation can cause genetic degradation and or rising resistance against food pathogens or antimicrobial substances they produce. For this objective, a newly isolated strain of Lactobacillus acidophilus possessing high antimicrobial activity was evaluated as a candidate for use in biopreservation.Materials and Methods: Antibacterial activity was evaluated by agar disk diffusion method. Hydrogen peroxide amount was measured by Merckoquant Peroxide test strips. Microbiological analysis of the ground beef infected by Escherichia coli O157:H7 and treated by Lactobacillus acidophilus GH 201was done by plating of serial dilution in physiological saline on Tryptose agar.Results and Conclusion: The cells (109 CFU ml-1 of Lactobacillus acidophilus produced significant amount of antibacterial substances mainly hydrogen peroxide (28 and 30 μg ml-1 in sodium phosphate buffer (0.2 M, pH 6.5 and LAPTg at 5°C during submerged cultivation with no growth, respectively. Submerged co-cultivation of Escherichia coli O157:H7 with lactobacilli in LAPTg broth at 5°C reduced the total number of the pathogen more than 2 log for 5 days. In case of solid state cultivation on agar-based medium, the maximum inhibitory zones on Escherichia coli O157:H7 lawn around the disks soaked by different amounts of washed Lactobacillus acidophilus cells appear for one-day cold exposition. The size of inhibition zone depends on the concentration of lactic acid bacteria cells. The cell suspension intended for treatment must contain 108-9CFU ml-1 of lactic acid bacteria. Lactobacillus acidophilus reduced the initial amount (2×105 CFU ml-1 of Escherichia coli O157:H7 in ground beef up to 2 log for 5 days of solid-state co-cultivation. The application of Lactobacillus acidophilus bacteria expanded the shelf-life of ground beef due to inhibition of

  5. The incidence and antibiotics susceptibility of Escherichia coli O157 ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-02-22

    Feb 22, 2010 ... The incidence of Escherichia coli 0157: H7 was assessed in meat samples from slaughtered cattle in. Ibadan metropolis by culturing ... high quality farm to fork wholesome and safe meat for public consumption in Nigeria. Key words: EHEC .... Prevalence and in vitro antimicrobial susceptibility. Trop. Vet. 26.

  6. Induction of genetic recombination in the lambda bacteriophage by ultraviolet radiation of the Escherichia Coli cells; Induccion de recombinacion genetica en el bacteriofago lambda por irradiacion ultravioleta de las cellulas de Escherichia Coli

    Energy Technology Data Exchange (ETDEWEB)

    Alcantara D, D [ININ, 52045 Ocoyoacac, Estado de Mexico (Mexico)

    1986-12-15

    In this work there are reported the results that show that although the stimulation of the recombination of the Lambda bacteriophage, by UV irradiation of the cells of Escherichia Coli, it looks to be the result of the high expression of the functions of the SOS system, doesn't keep some relationship with the high concentration of protein reached RecA. (Author)

  7. Induction of genetic recombination in the lambda bacteriophage by ultraviolet radiation of the Escherichia Coli cells; Induccion de recombinacion genetica en el bacteriofago lambda por irradiacion ultravioleta de las cellulas de Escherichia Coli

    Energy Technology Data Exchange (ETDEWEB)

    Alcantara D, D. [ININ, 52045 Ocoyoacac, Estado de Mexico (Mexico)

    1986-12-15

    In this work there are reported the results that show that although the stimulation of the recombination of the Lambda bacteriophage, by UV irradiation of the cells of Escherichia Coli, it looks to be the result of the high expression of the functions of the SOS system, doesn't keep some relationship with the high concentration of protein reached RecA. (Author)

  8. [Construction and characterization of enterohemorrhagic Escherichia coli O157:H7 ppk- deleted strain].

    Science.gov (United States)

    Han, Peng; Sun, Qi; Zhao, Suhui; Zhang, Qiwei; Wan, Chengsong

    2014-06-01

    To construct enterohemorrhagic Escherichia coli (EHEC) O157: H7 ppk gene deletion strains and study its biological characteristics. The gene fragment of kanamycin resistance was amplified using a pair of homologous arm primers whose 5' and 3' ends were homologous with ppk gene and kanamycin resistance gene, respectively. EHEC O157: H7 EDL933w competent strains were prepared and transformed via electroporation with the amplification products. The ppk gene was replaced by kanamycin resistance gene using pKD46-mediated Red recombination system. The recombinant strain was confirmed by PCR and sequencing, and its morphology, growth ability and adhesion were assessed using Gram staining, OD600 value and Giemsa staining. We established a ppk-deleted EHEC O157:H7 EDL933w strain with kanamycin resistance and compared the biological characteristics of the wild-type and mutant strains, which may facilitate further study of the regulatory mechanism of ppk gene.

  9. Inactivation of Escherichia coli O157:H7 in vitro and on the surface of spinach leaves by biobased surfactants

    Science.gov (United States)

    This study was conducted to evaluate the effect of biosurfactants on the populations of Escherichia coli O157:H7 in suspension and on spinach leaves. Eight surfactants including four soybean oil-based biosurfactants, sodium dodecyl sulfate (SDS), polyoxyethylene sorbitan monooleate (Tween 80), sopho...

  10. PLACD-7T Study: Atherosclerotic Carotid Plaque Components Correlated with Cerebral Damage at 7 Tesla Magnetic Resonance Imaging.

    Science.gov (United States)

    den Hartog, A G; Bovens, S M; Koning, W; Hendrikse, J; Pasterkamp, G; Moll, F L; de Borst, G J

    2011-02-01

    In patients with carotid artery stenosis histological plaque composition is associated with plaque stability and with presenting symptomatology. Preferentially, plaque vulnerability should be taken into account in pre-operative work-up of patients with severe carotid artery stenosis. However, currently no appropriate and conclusive (non-) invasive technique to differentiate between the high and low risk carotid artery plaque in vivo is available. We propose that 7 Tesla human high resolution MRI scanning will visualize carotid plaque characteristics more precisely and will enable correlation of these specific components with cerebral damage. The aim of the PlaCD-7T study is 1: to correlate 7T imaging with carotid plaque histology (gold standard); and 2: to correlate plaque characteristics with cerebral damage ((clinically silent) cerebral (micro) infarcts or bleeds) on 7 Tesla high resolution (HR) MRI. We propose a single center prospective study for either symptomatic or asymptomatic patients with haemodynamic significant (70%) stenosis of at least one of the carotid arteries. The Athero-Express (AE) biobank histological analysis will be derived according to standard protocol. Patients included in the AE and our prospective study will undergo a pre-operative 7 Tesla HR-MRI scan of both the head and neck area. We hypothesize that the 7 Tesla MRI scanner will allow early identification of high risk carotid plaques being associated with micro infarcted cerebral areas, and will thus be able to identify patients with a high risk of periprocedural stroke, by identification of surrogate measures of increased cardiovascular risk.

  11. PLACD-7T Study: Atherosclerotic Carotid Plaque Components Correlated with Cerebral Damage at 7 Tesla Magnetic Resonance Imaging

    Science.gov (United States)

    den Hartog, A.G; Bovens, S.M; Koning, W; Hendrikse, J; Pasterkamp, G; Moll, F.L; de Borst, G.J

    2011-01-01

    Introduction: In patients with carotid artery stenosis histological plaque composition is associated with plaque stability and with presenting symptomatology. Preferentially, plaque vulnerability should be taken into account in pre-operative work-up of patients with severe carotid artery stenosis. However, currently no appropriate and conclusive (non-) invasive technique to differentiate between the high and low risk carotid artery plaque in vivo is available. We propose that 7 Tesla human high resolution MRI scanning will visualize carotid plaque characteristics more precisely and will enable correlation of these specific components with cerebral damage. Study objective: The aim of the PlaCD-7T study is 1: to correlate 7T imaging with carotid plaque histology (gold standard); and 2: to correlate plaque characteristics with cerebral damage ((clinically silent) cerebral (micro) infarcts or bleeds) on 7 Tesla high resolution (HR) MRI. Design: We propose a single center prospective study for either symptomatic or asymptomatic patients with haemodynamic significant (70%) stenosis of at least one of the carotid arteries. The Athero-Express (AE) biobank histological analysis will be derived according to standard protocol. Patients included in the AE and our prospective study will undergo a pre-operative 7 Tesla HR-MRI scan of both the head and neck area. Discussion: We hypothesize that the 7 Tesla MRI scanner will allow early identification of high risk carotid plaques being associated with micro infarcted cerebral areas, and will thus be able to identify patients with a high risk of periprocedural stroke, by identification of surrogate measures of increased cardiovascular risk. PMID:22294972

  12. Identification of novel substrates of Shigella T3SA through analysis of its virulence plasmid-encoded secretome

    Science.gov (United States)

    Pinaud, Laurie; Ferrari, Mariana L.; Friedman, Robin; Jehmlich, Nico; von Bergen, Martin; Phalipon, Armelle; Sansonetti, Philippe J.

    2017-01-01

    Many human Gram-negative bacterial pathogens express a Type Three Secretion Apparatus (T3SA), including among the most notorious Shigella spp., Salmonella enterica, Yersinia enterocolitica and enteropathogenic Escherichia coli (EPEC). These bacteria express on their surface multiple copies of the T3SA that mediate the delivery into host cells of specific protein substrates critical to pathogenesis. Shigella spp. are Gram-negative bacterial pathogens responsible for human bacillary dysentery. The effector function of several Shigella T3SA substrates has largely been studied but their potential cellular targets are far from having been comprehensively delineated. In addition, it is likely that some T3SA substrates have escaped scrutiny as yet. Indeed, sequencing of the virulence plasmid of Shigella flexneri has revealed numerous open reading frames with unknown functions that could encode additional T3SA substrates. Taking advantage of label-free mass spectrometry detection of proteins secreted by a constitutively secreting strain of S. flexneri, we identified five novel substrates of the T3SA. We further confirmed their secretion through the T3SA and translocation into host cells using β-lactamase assays. The coding sequences of two of these novel T3SA substrates (Orf13 and Orf131a) have a guanine-cytosine content comparable to those of T3SA components and effectors. The three other T3SA substrates identified (Orf48, Orf86 and Orf176) have significant homology with antitoxin moieties of type II Toxin-Antitoxin systems usually implicated in the maintenance of low copy plasmids. While Orf13 and Orf131a might constitute new virulence effectors contributing to S. flexneri pathogenicity, potential roles for the translocation into host cells of antitoxins or antitoxin-like proteins during Shigella infection are discussed. PMID:29073283

  13. Identification of novel substrates of Shigella T3SA through analysis of its virulence plasmid-encoded secretome.

    Directory of Open Access Journals (Sweden)

    Laurie Pinaud

    Full Text Available Many human Gram-negative bacterial pathogens express a Type Three Secretion Apparatus (T3SA, including among the most notorious Shigella spp., Salmonella enterica, Yersinia enterocolitica and enteropathogenic Escherichia coli (EPEC. These bacteria express on their surface multiple copies of the T3SA that mediate the delivery into host cells of specific protein substrates critical to pathogenesis. Shigella spp. are Gram-negative bacterial pathogens responsible for human bacillary dysentery. The effector function of several Shigella T3SA substrates has largely been studied but their potential cellular targets are far from having been comprehensively delineated. In addition, it is likely that some T3SA substrates have escaped scrutiny as yet. Indeed, sequencing of the virulence plasmid of Shigella flexneri has revealed numerous open reading frames with unknown functions that could encode additional T3SA substrates. Taking advantage of label-free mass spectrometry detection of proteins secreted by a constitutively secreting strain of S. flexneri, we identified five novel substrates of the T3SA. We further confirmed their secretion through the T3SA and translocation into host cells using β-lactamase assays. The coding sequences of two of these novel T3SA substrates (Orf13 and Orf131a have a guanine-cytosine content comparable to those of T3SA components and effectors. The three other T3SA substrates identified (Orf48, Orf86 and Orf176 have significant homology with antitoxin moieties of type II Toxin-Antitoxin systems usually implicated in the maintenance of low copy plasmids. While Orf13 and Orf131a might constitute new virulence effectors contributing to S. flexneri pathogenicity, potential roles for the translocation into host cells of antitoxins or antitoxin-like proteins during Shigella infection are discussed.

  14. High-pressure synthesis and characterization of the effective pseudospin S =1 /2 XY pyrochlores R2P t2O7 (R =Er ,Yb )

    Science.gov (United States)

    Cai, Y. Q.; Cui, Q.; Li, X.; Dun, Z. L.; Ma, J.; dela Cruz, C.; Jiao, Y. Y.; Liao, J.; Sun, P. J.; Li, Y. Q.; Zhou, J. S.; Goodenough, J. B.; Zhou, H. D.; Cheng, J.-G.

    2016-01-01

    We report on the high-pressure syntheses and detailed characterizations of two effective pseudospin S =1 /2 XY pyrochlores E r2P t2O7 and Y b2P t2O7 via x-ray/neutron powder diffraction, dc and ac magnetic susceptibility, and specific-heat measurements down to 70 mK. We found that both compounds undergo long-range magnetic transitions at TN ,C≈0.3 K , which are ascribed to an antiferromagnetic- and ferromagnetic-type order for E r2P t2O7 and Y b2P t2O7 , respectively, based on the field dependence of their transition temperatures as well as the systematic comparisons with other similar pyrochlores R2B2O7 (R =Er ,Yb ;B =Sn ,Ti ,Ge ). The observed TN of E r2P t2O7 is much lower than that expected from the relationship of TN versus the ionic radius of B4 + derived from the series of E r2B2O7 , while the TC of Y b2P t2O7 is the highest among the series of ferromagnetic compounds Y b2B2O7 (B =Sn ,Pt ,Ti ). Given the monotonic variation of the lattice constant as a function of the B -cation size across these two series of R2B2O7 (R =Er ,Yb ), the observed anomalous values of TN ,C in the Pt-based XY pyrochlores imply that another important factor beyond the nearest-neighbor R -R distance is playing a role. In light of the anisotropic exchange interactions Jex={Jz z,J±,J±±,Jz ± } for the S =1 /2 XY pyrochlores, we have rationalized these observations by considering a weakened (enhanced) antiferromagnetic planar J± (ferromagnetic Ising-like Jz z) due to strong Pt 5 d -O 2 p hybridization within the plane perpendicular to the local [111] direction.

  15. How bio-questionable are the different recombinant human erythropoietin copy products in Thailand?

    Science.gov (United States)

    Halim, Liem Andhyk; Brinks, Vera; Jiskoot, Wim; Romeijn, Stefan; Praditpornsilpa, Kearkiat; Assawamakin, Anunchai; Schellekens, Huub

    2014-05-01

    The high prevalence of pure red cell aplasia in Thailand has been associated with the sharp increase in number of recombinant human erythropoietin (rhEPO) copy products, based on a classical generic regulatory pathway, which have entered the market. This study aims to assess the quality of rhEPO copy products being used in Thailand. Twelve rhEPO copy products were purchased from pharmacies in Thailand, shipped under controlled cold chain conditions to the Netherlands and characterized using (1) high performance size-exclusion chromatography, (2) asymmetrical flow field-flow fractionation, (3) sodium dodecyl sulfate polyacrylamide gel electrophoresis in combination with (4) Western blotting and additionally tested for (5) host cell protein impurities as well as (6) endotoxin contamination. Some of the tested rhEPO copy products showed high aggregate levels and contained a substantial amount of protein fragments. Also, one of rhEPO copy products had a high endotoxin level, exceeding the FDA limit. Our observations show that some of the tested copy products on the Thai market differ significantly from the originator rhEPO product, Epogen®. This comparison study supports a link between the quality attributes of copy rhEPO products and their immunogenicity.

  16. Transcriptome Changes of Escherichia coli, Enterococcus faecalis, and Escherichia coli O157:H7 Laboratory Strains in Response to Photo-Degraded DOM

    Directory of Open Access Journals (Sweden)

    Adelumola Oladeinde

    2018-05-01

    Full Text Available In this study, we investigated gene expression changes in three bacterial strains (Escherichia coli C3000, Escherichia coli O157:H7 B6914, and Enterococcus faecalis ATCC 29212, commonly used as indicators of water quality and as control strains in clinical, food, and water microbiology laboratories. Bacterial transcriptome responses from pure cultures were monitored in microcosms containing water amended with manure-derived dissolved organic matter (DOM, previously exposed to simulated sunlight for 12 h. We used RNA sequencing (RNA-seq and quantitative real-time reverse transcriptase (qRT-PCR to compare differentially expressed temporal transcripts between bacteria incubated in microcosms containing sunlight irradiated and non-irradiated DOM, for up to 24 h. In addition, we used whole genome sequencing simultaneously with RNA-seq to identify single nucleotide variants (SNV acquired in bacterial populations during incubation. These results indicate that E. coli and E. faecalis have different mechanisms for removal of reactive oxygen species (ROS produced from irradiated DOM. They are also able to produce micromolar concentrations of H2O2 from non-irradiated DOM, that should be detrimental to other bacteria present in the environment. Notably, this study provides an assessment of the role of two conjugative plasmids carried by the E. faecalis and highlights the differences in the overall survival dynamics of environmentally-relevant bacteria in the presence of naturally-produced ROS.

  17. Genome-wide copy number variation (CNV) in patients with autoimmune Addison's disease

    Science.gov (United States)

    2011-01-01

    Background Addison's disease (AD) is caused by an autoimmune destruction of the adrenal cortex. The pathogenesis is multi-factorial, involving genetic components and hitherto unknown environmental factors. The aim of the present study was to investigate if gene dosage in the form of copy number variation (CNV) could add to the repertoire of genetic susceptibility to autoimmune AD. Methods A genome-wide study using the Affymetrix GeneChip® Genome-Wide Human SNP Array 6.0 was conducted in 26 patients with AD. CNVs in selected genes were further investigated in a larger material of patients with autoimmune AD (n = 352) and healthy controls (n = 353) by duplex Taqman real-time polymerase chain reaction assays. Results We found that low copy number of UGT2B28 was significantly more frequent in AD patients compared to controls; conversely high copy number of ADAM3A was associated with AD. Conclusions We have identified two novel CNV associations to ADAM3A and UGT2B28 in AD. The mechanism by which this susceptibility is conferred is at present unclear, but may involve steroid inactivation (UGT2B28) and T cell maturation (ADAM3A). Characterization of these proteins may unravel novel information on the pathogenesis of autoimmunity. PMID:21851588

  18. Genome-wide copy number variation (CNV in patients with autoimmune Addison's disease

    Directory of Open Access Journals (Sweden)

    Brønstad Ingeborg

    2011-08-01

    Full Text Available Abstract Background Addison's disease (AD is caused by an autoimmune destruction of the adrenal cortex. The pathogenesis is multi-factorial, involving genetic components and hitherto unknown environmental factors. The aim of the present study was to investigate if gene dosage in the form of copy number variation (CNV could add to the repertoire of genetic susceptibility to autoimmune AD. Methods A genome-wide study using the Affymetrix GeneChip® Genome-Wide Human SNP Array 6.0 was conducted in 26 patients with AD. CNVs in selected genes were further investigated in a larger material of patients with autoimmune AD (n = 352 and healthy controls (n = 353 by duplex Taqman real-time polymerase chain reaction assays. Results We found that low copy number of UGT2B28 was significantly more frequent in AD patients compared to controls; conversely high copy number of ADAM3A was associated with AD. Conclusions We have identified two novel CNV associations to ADAM3A and UGT2B28 in AD. The mechanism by which this susceptibility is conferred is at present unclear, but may involve steroid inactivation (UGT2B28 and T cell maturation (ADAM3A. Characterization of these proteins may unravel novel information on the pathogenesis of autoimmunity.

  19. High spatial resolution and temporally resolved T2* mapping of normal human myocardium at 7.0 Tesla: an ultrahigh field magnetic resonance feasibility study.

    Directory of Open Access Journals (Sweden)

    Fabian Hezel

    Full Text Available Myocardial tissue characterization using T(2(* relaxation mapping techniques is an emerging application of (preclinical cardiovascular magnetic resonance imaging. The increase in microscopic susceptibility at higher magnetic field strengths renders myocardial T(2(* mapping at ultrahigh magnetic fields conceptually appealing. This work demonstrates the feasibility of myocardial T(2(* imaging at 7.0 T and examines the applicability of temporally-resolved and high spatial resolution myocardial T(2(* mapping. In phantom experiments single cardiac phase and dynamic (CINE gradient echo imaging techniques provided similar T(2(* maps. In vivo studies showed that the peak-to-peak B(0 difference following volume selective shimming was reduced to approximately 80 Hz for the four chamber view and mid-ventricular short axis view of the heart and to 65 Hz for the left ventricle. No severe susceptibility artifacts were detected in the septum and in the lateral wall for T(2(* weighting ranging from TE = 2.04 ms to TE = 10.2 ms. For TE >7 ms, a susceptibility weighting induced signal void was observed within the anterior and inferior myocardial segments. The longest T(2(* values were found for anterior (T(2(* = 14.0 ms, anteroseptal (T(2(* = 17.2 ms and inferoseptal (T(2(* = 16.5 ms myocardial segments. Shorter T(2(* values were observed for inferior (T(2(* = 10.6 ms and inferolateral (T(2(* = 11.4 ms segments. A significant difference (p = 0.002 in T(2(* values was observed between end-diastole and end-systole with T(2(* changes of up to approximately 27% over the cardiac cycle which were pronounced in the septum. To conclude, these results underscore the challenges of myocardial T(2(* mapping at 7.0 T but demonstrate that these issues can be offset by using tailored shimming techniques and dedicated acquisition schemes.

  20. The Art of Copying

    DEFF Research Database (Denmark)

    Christensen, Hans Dam

    2017-01-01

    This article discusses copies within the field of art museums by way of mapping strategies for copy practices. This mapping leans heavily towards parts of the writings of Jacques Derrida (1930–2004). Against the backdrop of this theoretical premise, the article distinguishes five main strategies....... An informational copy is just as unique as an original object of art, and at the same time, it defines the original and is itself defined by this opposition. Lastly, the strategy for the imagined relation between original and copy follows. This strategy is dependent upon several of the previous approaches, and...

  1. Whole brain, high resolution multiband spin-echo EPI fMRI at 7 T: A comparison with gradient-echo EPI using a color-word Stroop task

    NARCIS (Netherlands)

    Boyacioglu, R.; Schulz, J.; Müller, N.C.J.; Koopmans, P.J.; Barth, M.; Norris, David Gordon

    2014-01-01

    A whole brain, multiband spin-echo (SE) echo planar imaging (EPI) sequence employing a high spatial (1.5 mm isotropic) and temporal (TR of 2 s) resolution was implemented at 7 T. Its overall performance (tSNR, sensitivity and CNR) was assessed and compared to a geometrically matched gradient-echo

  2. The Protein Interaction Network of Bacteriophage Lambda with Its Host, Escherichia coli

    Science.gov (United States)

    Blasche, Sonja; Wuchty, Stefan; Rajagopala, Seesandra V.

    2013-01-01

    Although most of the 73 open reading frames (ORFs) in bacteriophage λ have been investigated intensively, the function of many genes in host-phage interactions remains poorly understood. Using yeast two-hybrid screens of all lambda ORFs for interactions with its host Escherichia coli, we determined a raw data set of 631 host-phage interactions resulting in a set of 62 high-confidence interactions after multiple rounds of retesting. These links suggest novel regulatory interactions between the E. coli transcriptional network and lambda proteins. Targeted host proteins and genes required for lambda infection are enriched among highly connected proteins, suggesting that bacteriophages resemble interaction patterns of human viruses. Lambda tail proteins interact with both bacterial fimbrial proteins and E. coli proteins homologous to other phage proteins. Lambda appears to dramatically differ from other phages, such as T7, because of its unusually large number of modified and processed proteins, which reduces the number of host-virus interactions detectable by yeast two-hybrid screens. PMID:24049175

  3. Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease

    Science.gov (United States)

    Aldhous, Marian C.; Abu Bakar, Suhaili; Prescott, Natalie J.; Palla, Raquel; Soo, Kimberley; Mansfield, John C.; Mathew, Christopher G.; Satsangi, Jack; Armour, John A.L.

    2010-01-01

    The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case–control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case–control studies. PMID:20858604

  4. Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease.

    Science.gov (United States)

    Aldhous, Marian C; Abu Bakar, Suhaili; Prescott, Natalie J; Palla, Raquel; Soo, Kimberley; Mansfield, John C; Mathew, Christopher G; Satsangi, Jack; Armour, John A L

    2010-12-15

    The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case-control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case-control studies.

  5. Robust Adaptable Video Copy Detection

    DEFF Research Database (Denmark)

    Assent, Ira; Kremer, Hardy

    2009-01-01

    in contrast). Our query processing combines filtering and indexing structures for efficient multistep computation of video copies under this model. We show that our model successfully identifies altered video copies and does so more reliably than existing models.......Video copy detection should be capable of identifying video copies subject to alterations e.g. in video contrast or frame rates. We propose a video copy detection scheme that allows for adaptable detection of videos that are altered temporally (e.g. frame rate change) and/or visually (e.g. change...

  6. Identification and utilization of cleistogamy gene cl7(t) in rice (Oryza sativa L.).

    Science.gov (United States)

    Ni, Da-Hu; Li, Juan; Duan, Yong-Bo; Yang, Ya-Chun; Wei, Peng-Cheng; Xu, Rong-Fang; Li, Chun-Rong; Liang, Dan-Dan; Li, Hao; Song, Feng-Shun; Ni, Jin-Long; Li, Li; Yang, Jian-Bo

    2014-05-01

    Gene transformation is an important method for improvement of plants into elite varieties. However, the possibility of gene flow between genetically modified (GM) crops and similar species is a serious public issue that may potentially endanger ecological stability. Cleistogamy is expected to be an ideal genetic tool for preventing transgene propagation from GM crops. A rice mutant, cl7(t), was created by ethyl methanesulfonate mutagenesis. The mutant exhibited cleistogamy, and had closed spikelets, reduced plant height, and altered morphology of the leaves, panicle, and seeds. Anatomical investigations revealed that the cl7(t) mutant contained more vascular bundles and thicker stems than the wild type, which increased the mechanical strength of its internodes, and anti-lodging ability. Further studies demonstrated that the force required to open the lemma and palea was higher in the cl7(t) mutant, and there was weak swelling ability in the lodicules, which leads to cleistogamy. Allelic analyses and complementation tests indicated that cl7(t) was a novel allele of dep2, a mutant that was previously reported to have similar panicle morphology. Sequence analysis showed that cl7(t) had a single nucleotide substitution (C to A) in the third exon that leads to a Ser substitution with a stop codon, giving a truncated DEP2 protein. Quantitative RT-PCR and in situ hybridization tests demonstrated that there was lower CL7(t) expression level in the spikelets and weaker CL7(t) signals in the lodicules of the cl7(t) mutant compared with wild type, which implies that CL7(t) might participate in the development of lodicules. To improve the agronomic traits of cl7(t) to fit the needs of field production, the cl7(t) mutant was crossed with an intermediate-type rice variety named Guanghui102, which bears some important agronomic traits, including increased grain numbers and high rate of seed setting. Through multi-generational pedigree selection, cleistogamy lines with improved

  7. Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

    Science.gov (United States)

    Carpenter, Danielle; Mitchell, Laura M; Armour, John A L

    2017-02-20

    Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes. AMY1 copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance, P structure may affect expression, but this was not significant in our data.

  8. Comparison of 3T and 7T susceptibility-weighted angiography of the substantia nigra in diagnosing Parkinson disease.

    Science.gov (United States)

    Cosottini, M; Frosini, D; Pesaresi, I; Donatelli, G; Cecchi, P; Costagli, M; Biagi, L; Ceravolo, R; Bonuccelli, U; Tosetti, M

    2015-03-01

    Standard neuroimaging fails in defining the anatomy of the substantia nigra and has a marginal role in the diagnosis of Parkinson disease. Recently 7T MR target imaging of the substantia nigra has been useful in diagnosing Parkinson disease. We performed a comparative study to evaluate whether susceptibility-weighted angiography can diagnose Parkinson disease with a 3T scanner. Fourteen patients with Parkinson disease and 13 healthy subjects underwent MR imaging examination at 3T and 7T by using susceptibility-weighted angiography. Two expert blinded observers and 1 neuroradiology fellow evaluated the 3T and 7T images of the sample to identify substantia nigra abnormalities indicative of Parkinson disease. Diagnostic accuracy and intra- and interobserver agreement were calculated separately for 3T and 7T acquisitions. Susceptibility-weighted angiography 7T MR imaging can diagnose Parkinson disease with a mean sensitivity of 93%, specificity of 100%, and diagnostic accuracy of 96%. 3T MR imaging diagnosed Parkinson disease with a mean sensitivity of 79%, specificity of 94%, and diagnostic accuracy of 86%. Intraobserver and interobserver agreement was excellent at 7T. At 3T, intraobserver agreement was excellent for experts, and interobserver agreement ranged between good and excellent. The less expert reader obtained a diagnostic accuracy of 89% at 3T. Susceptibility-weighted angiography images obtained at 3T and 7T differentiate controls from patients with Parkinson disease with a higher diagnostic accuracy at 7T. The capability of 3T in diagnosing Parkinson disease might encourage its use in clinical practice. The use of the more accurate 7T should be supported by a dedicated cost-effectiveness study. © 2015 by American Journal of Neuroradiology.

  9. Global chromosomal structural instability in a subpopulation of starving Escherichia coli cells.

    Directory of Open Access Journals (Sweden)

    Dongxu Lin

    2011-08-01

    Full Text Available Copy-number variations (CNVs constitute very common differences between individual humans and possibly all genomes and may therefore be important fuel for evolution, yet how they form remains elusive. In starving Escherichia coli, gene amplification is induced by stress, controlled by the general stress response. Amplification has been detected only encompassing genes that confer a growth advantage when amplified. We studied the structure of stress-induced gene amplification in starving cells in the Lac assay in Escherichia coli by array comparative genomic hybridization (aCGH, with polymerase chain reaction (pcr and DNA sequencing to establish the structures generated. About 10% of 300 amplified isolates carried other chromosomal structural change in addition to amplification. Most of these were inversions and duplications associated with the amplification event. This complexity supports a mechanism similar to that seen in human non-recurrent copy number variants. We interpret these complex events in terms of repeated template switching during DNA replication. Importantly, we found a significant occurrence (6 out of 300 of chromosomal structural changes that were apparently not involved in the amplification event. These secondary changes were absent from 240 samples derived from starved cells not carrying amplification, suggesting that amplification happens in a differentiated subpopulation of stressed cells licensed for global chromosomal structural change and genomic instability. These data imply that chromosomal structural changes occur in bursts or showers of instability that may have the potential to drive rapid evolution.

  10. Inactivation of Escherichia coli in broth and sausage by combined high pressure and Lactobacillus casei cell extract.

    Science.gov (United States)

    Chung, Hyun-Jung; Yousef, Ahmed E

    2010-10-01

    The purpose of this study was to investigate the effect of combined high pressure and Lactobacillus casei cell extract (CE) on Escherichia coli O157 strains with variation in pressure resistance in broth and sausage. Pressure-resistant (O157:H7 and O157:H12) and -sensitive (O157-M1 and O157-M2) E. coli strains were used. Pressure treatment at 350 MPa for 20 min in broth caused 1.1-1.2 logs reduction in O157:H12 and O157:H7 and 4.1-5.5 logs reduction in the O157-M1 and O157-M2. When high pressure was treated in the presence of CE (32 CEAU/mL), the combination treatment caused a significant inactivation in the pressure-resistant O157:H7 strains resulting in the viability loss of 4.3-4.6 logs and the synergistic effect increased with increase in treatment time (p casei CE may cause considerable damage to cellular components of E. coli during the high pressure treatment. The synergy between high pressure processing and Lb. casei OSY-LB6A CE against pressure-resistant E. coli O157 strains suggests the feasibility of using this combination to minimize the risk of transmission of E. coli O157 by food.

  11. Role of major surface structures of Escherichia coli O157:H7 in initial attachment to biotic and abiotic surfaces

    Science.gov (United States)

    Infection by human pathogens through fresh, minimally processed produce and solid plant-derived foods is a major concern of U.S. and global food industry and public health services. The enterohemorrhagic Escherichia coli O157:H7 is a frequent and potent food borne pathogen that causes severe disease...

  12. Recovery of the accumulation ability of thiomethyl-β-galactoside in Escherichia coli after bacteriophage T4 infection

    International Nuclear Information System (INIS)

    Saijo, N.; Okamoto, K.

    1976-01-01

    Effects of uv-irradiated and unirradiated T4 phage infection on the β-galactoside accumulation ability in Escherichia coli have been examined by the use of 14 C-labeled thiomethyl-β-galactoside (TMG). Under conditions where a synchronous adsorption of phage takes place, the cellular ability for TMG accumulation is found to be largely inhibited immediately after phage adsorption but it recovers with time to a new level, which is dependent on the multiplicity of infection. When cells are infected with uv-irradiated T4 at the same multiplicity as that of unirradiated phage, the cellular accumulation ability is more severely inhibited and there is no recovery from the inhibition. The recovery process in T4-infected cells is mostly sensitive to puromycin. These results suggest that the initial inhibition of the TMG accumulation ability is probably caused by the adsorption of phage coats, and the subsequent restoration occurs through the action of a phage-directed protein(s). In the recovery process, no new transport system appears to be involved. The restored ability of TMG accumulation is resistant to the action of superinfecting uv phage. However, different mechanisms appear to be operating in T4-infected cells for the establishment of resistance to ghosts and for the recovery from the phage coat-induced inhibition

  13. Dielectric barrier discharge atmospheric cold plasma inhibits Escherichia coli 0157:H7, Salmonella, Listeria monocytogenes, and Tulane virus in Romaine lettuce

    Science.gov (United States)

    The present study investigated the effects of dielectric barrier discharge atmospheric cold plasma (DACP) treatment on the inactivation of Escherichia coli O157:H7, Salmonella, Listeria monocytogenes, and Tulane virus (TV) on Romaine lettuce, assessing the influences of moisture vaporization, modifi...

  14. Vortex transport entropy in the H-T diagram of high T{sub c} superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Bridoux, G; Nieva, G; Cruz, F de la, E-mail: gbridoux@yahoo.com.a [Centro Atomico Bariloche and Instituto Balseiro, Comision Nacional de Energia Atomica, Av. E. Bustillo 9500, R84002AGP S. C. de Bariloche (Argentina)

    2009-05-01

    The combination of Nernst effect and electrical resistivity measurements allows to extract the transport entropy carried by moving vortices. In high T{sub c} superconductors, the vortex-like fluctuations close and above T{sub c} can be detected with these tools if local phase coherence is still present. In this work we study the vortex transport entropy in the two milestone high T{sub c}, YBa{sub 2}Cu{sub 3}O{sub 7-d}elta (YBCO) and Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+d}elta (BSCCO). While below T{sub c} the YBCO entropy displays a mean field like behavior, close and above T{sub c} the entropy reveals typical features of strong superconducting fluctuations. The lower dimensionality in BSCCO enhances the strength of superconducting fluctuations in a wider region of the H - Tdiagram and a mean field treatment can not be applied. In this region the vortex transport entropy remains unaffected by the presence of correlated defects.

  15. Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Hiraku Takada

    Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons

  16. Hard-copy versus soft-copy with and without simple image manipulation for detection of pulmonary nodules and masses

    International Nuclear Information System (INIS)

    Kosuda, S.; Kaji, T.; Iwasaki, Y.; Kusano, S.; Kobayashi, H.; Watanabe, M.

    2000-01-01

    To compare interpretation performance on soft-copy presentations, with and without simple image manipulation, and on unmodified hard-copy presentations with regard to detection of pulmonary nodules and masses. Material and Methods: Fifty chest digital radiograph combinations of patients with a total of 60 nodules, 32 of which were 2.0 cm in diameter, were selected for the study. Three readers evaluated three separate image formats: unmodified hard- and soft-copies, and soft-copies with simple image manipulation of lung and mediastinum window settings, and zooming. The screen display was 1600x1200 pixels with 8 bits/pixel. Results: The sensitivity, accuracy, detectability, and Az value of the soft-copy systems were clearly inferior to hard-copy evaluation. The mean Az values were 0.921 for unmodified hard-copy, 0.820 for image-manipulated soft-copy, and 0.781 for unmodified soft-copy. Conclusion: Soft-copy interpretations were not as sensitive in detecting pulmonary nodules and masses as hard-copy evaluation

  17. Overexpression of IL-7R alpha provides a competitive advantage during early T-cell development.

    Science.gov (United States)

    Laouar, Yasmina; Crispe, I Nicholas; Flavell, Richard A

    2004-03-15

    Critical checkpoints controlling early thymic T-cell development and homeostasis are set by the proper signaling function of the interleukin 7 receptor (IL-7R) and the pre-T-cell antigen receptor. Although alpha beta T-cell development is observed in IL-7- and IL-7R alpha-deficient mice, the number of thymocytes is significantly reduced, implying a role for the IL-7R in controlling the size of the thymic T-cell compartment. Here, we report the overexpression of IL-7R alpha that occurs in the early T-cell compartment from AKR/J mice, animals that are highly susceptible to the spontaneous development of thymoma. Increased IL-7R alpha was revealed by surface staining, and increased IL-7R alpha mRNA was documented by using reverse transcriptase-polymerase chain reaction (RT-PCR). This resulted in increased survival of AKR/J early thymocytes, shown by the decreased frequency of TUNEL(+) (terminal deoxynucleotidyl transferase mediated deoxyuridine triphosphate [dUTP]-fluorescein nick end labeling) cells. In an in vivo thymocyte repopulation model, AKR/J thymocytes had a selective advantage over healthy thymocytes. This advantage occurred at early stages of T-cell development. Our findings support the model that overexpression of growth factor receptors can contribute to proliferation and malignancy.

  18. 77 FR 58091 - Risk-Based Sampling of Beef Manufacturing Trimmings for Escherichia coli (E. coli) O157:H7 and...

    Science.gov (United States)

    2012-09-19

    ... for exposure of carcasses and parts to any contamination or food safety hazard during the removal of... DEPARTMENT OF AGRICULTURE Food Safety and Inspection Service [Docket No. FSIS-2012-0020] Risk-Based Sampling of Beef Manufacturing Trimmings for Escherichia coli (E. coli) O157:H7 and Plans for Beef...

  19. Inactivation of Escherichia coli 0157:H7 and aerobic microorganisms in Romaine lettuce packaged in a commercial polyethylene terephthalate container using atmospheric cold plasma

    Science.gov (United States)

    The effects of dielectric barrier discharge atmospheric cold plasma (DACP) treatment on the inactivation of Escherichia coli O157:H7 and aerobic microorganisms in Romaine lettuce packaged in a conventional commercial plastic container were evaluated during storage at 4 degrees C for 7 days. Effects ...

  20. Comparison of U.S. Environmental Protection Agency and U.S. Composting Council... Escherichia coli O157:H7 in finished compost

    Science.gov (United States)

    Composting management or conditions that result in inadequate exposure of the compostable materials to destructive time-temperature regimens can result in survival of enteric human pathogens. Bacterial pathogens, such as Escherichia coli O157:H7 and Salmonella spp., can regrow in finished compost. ...

  1. A multi-pathogen selective enrichment broth for simultaneous growth of Salmonella enteria, Escherichia coli O157:H7 and Shigella flexneri

    Science.gov (United States)

    Salmonella, Shigella, and Escherichia coli O157:H7 contaminate similar types of food and all three can cause foodborne disease. Traditional microbiological enrichment broths to detect these pathogens are different in terms of their composition, which limits the application of multi-pathogen detectio...

  2. Design and Simulation of a Birdcage Coil using CST Studio Suite for Application at 7T

    International Nuclear Information System (INIS)

    Tomas, Bernat Palau; Li, Houmin; Anjum, M R

    2013-01-01

    This work describes the study of coils for Magnetic Resonance Imaging (MRI) applications. The principal objective is the design of a birdcage Radio Frequency (RF) coil to use in a 7 Tesla (7T) scanner. Higher strength field generates a better SNR and increased chemical shift effect, improving spectral fat suppression and spectroscopy. Moreover, a better SNR increases the spatial resolution or reduces the imaging time. This research work presented recent developments based on high field 7T design using CST studio. The birdcage coil achieves circular polarization and generates a high homogeneous radio frequency magnetic field under many conditions. Design of a Birdcage coil for a 7T to obtain the images from s mall animals (i.e. mouse). It opens the door to design and construct a Birdcage coil for a 7T to obtain human brain images. Firstly we design a birdcage coil then the results are obtained with simulator CST Wave Studio, creating a 3D model and generating a simulation. Finally the parameters are re adjusted to obtain our desired Larmor frequency 298.2 MHz for a correct operation in 7T. This research work demonstrates the theoretical results from our design and shows the designed antenna behavior

  3. Design and Simulation of a Birdcage Coil using CST Studio Suite for Application at 7T

    Science.gov (United States)

    Palau Tomas, Bernat; Li, Houmin; Anjum, M. R.

    2013-12-01

    This work describes the study of coils for Magnetic Resonance Imaging (MRI) applications. The principal objective is the design of a birdcage Radio Frequency (RF) coil to use in a 7 Tesla (7T) scanner. Higher strength field generates a better SNR and increased chemical shift effect, improving spectral fat suppression and spectroscopy. Moreover, a better SNR increases the spatial resolution or reduces the imaging time. This research work presented recent developments based on high field 7T design using CST studio. The birdcage coil achieves circular polarization and generates a high homogeneous radio frequency magnetic field under many conditions. Design of a Birdcage coil for a 7T to obtain the images from s mall animals (i.e. mouse). It opens the door to design and construct a Birdcage coil for a 7T to obtain human brain images. Firstly we design a birdcage coil then the results are obtained with simulator CST Wave Studio, creating a 3D model and generating a simulation. Finally the parameters are re adjusted to obtain our desired Larmor frequency 298.2 MHz for a correct operation in 7T. This research work demonstrates the theoretical results from our design and shows the designed antenna behavior.

  4. The DNA-mimic antirestriction proteins ArdA ColIB-P9, Arn T4, and Ocr T7 as activators of H-NS-dependent gene transcription.

    Science.gov (United States)

    Melkina, Olga E; Goryanin, Ignatiy I; Zavilgelsky, Gennadii B

    2016-11-01

    The antirestriction proteins ArdA ColIb-P9, Arn T4 and Ocr T7 specifically inhibit type I and type IV restriction enzymes and belong to the family of DNA-mimic proteins because their three-dimensional structure is similar to the double-helical B-form DNA. It is proposed that the DNA-mimic proteins are able to bind nucleoid protein H-NS and alleviate H-NS-silencing of the transcription of bacterial genes. Escherichia coli lux biosensors were constructed by inserting H-NS-dependent promoters into a vector, thereby placing each fragment upstream of the promoterless Photorhabdus luminescens luxCDABE operon. It was demonstrated that the DNA-mimic proteins ArdA, Arn and Ocr activate the transcription of H-NS-dependent promoters of the lux operon of marine luminescent bacteria (mesophilic Aliivibrio fischeri and psychrophilic Aliivibrio logei), and the dps gene from E. coli. It was also demonstrated that the ArdA antirestriction protein, the genes of which are located on transmissive plasmids ColIb-P9, R64, PK101, decreases levels of H-NS silencing of the PluxC promoter during conjugation in the recipient bacteria. Copyright © 2016 Elsevier GmbH. All rights reserved.

  5. Hydrotalcite formed by alteration of R7T7 nuclear waste glass and basaltic glass in salt brine at 190 degrees C

    International Nuclear Information System (INIS)

    Abdelouas, A.; Crovisier, J.L.; Lutze, W.; Mueller, R.; Bernotat, W.

    1994-01-01

    The R7T7 and synthetic basaltic glasses were submitted to corrosion in a saline MgCl 2 dominated solution at 190 degrees C. For both glasses, the early alteration product is a hydrotalcite-like compound in which HPO 4 2- , SO 4 2- and Cl - substitutes to CO 3 2- . The measured d 003 spacing is 7.68 angstrom for the hydrotalcite formed from R7T7 glass and 7.62 angstrom for the hydrotalcite formed from basaltic glass which reflect the high aluminium content. Chemical microanalyses show that the hydrotalcite is subsequently covered by a silica-rich gel which evolves into saponite after few months

  6. Persistence of Escherichia coli O157:H7 in dairy fermentation systems.

    Science.gov (United States)

    Dineen, S S; Takeuchi, K; Soudah, J E; Boor, K J

    1998-12-01

    We examined (i) the persistence of Escherichia coli O157:H7 as a postpasteurization contaminant in fermented dairy products; (ii) the ability of E. coli O157:H7 strains with and without the general stress regulatory protein, RpoS, to compete with commercial starter cultures in fermentation systems; and (iii) the survival of E. coli O157:H7 in the yogurt production process. In commercial products inoculated with 10(3) CFU/ml, E. coli O157:H7 was recovered for up to 12 days in yogurt (pH 4.0), 28 days in sour cream (pH 4.3), and at levels > 10(2) CFU/ml at 35 days in buttermilk (pH 4.1). For the starter culture competition trials, the relative inhibition of E. coli O157:H7 in the experimental fermentation systems was, in decreasing order, thermophilic culture mixture, Lactobacillus delbrueckii subsp. bulgaricus R110 alone, Lactococcus lactis subsp. lactis D280 alone, Lactococcus lactis subsp. cremoris D62 alone, and Streptococcus thermophilus C90 alone showing the least inhibition. Recovery of the rpoS mutant was lower than recovery of its wild-type parent by 72 h or earlier in the presence of individual starter cultures. No E. coli O157:H7 were recovered after the curd formation step in yogurt manufactured with milk inoculated with 10(5) CFU/ml. Our results show that (i) postprocessing entry of E. coli O157:H7 into fermented dairy products represents a potential health hazard; (ii) commercial starter cultures differ in their ability to reduce E. coli O157:H7 CFU numbers in fermentation systems; and (iii) the RpoS protein appears to most effectively contribute to bacterial survival in the presence of conditions that are moderately lethal to the cell.

  7. Copy number variation of KIR genes influences HIV-1 control

    DEFF Research Database (Denmark)

    Pelak, Kimberly; Need, Anna C; Fellay, Jacques

    2011-01-01

    A genome-wide screen for large structural variants showed that a copy number variant (CNV) in the region encoding killer cell immunoglobulin-like receptors (KIR) associates with HIV-1 control as measured by plasma viral load at set point in individuals of European ancestry. This CNV encompasses t...

  8. High-resolution copy number variation analysis of schizophrenia in Japan.

    Science.gov (United States)

    Kushima, I; Aleksic, B; Nakatochi, M; Shimamura, T; Shiino, T; Yoshimi, A; Kimura, H; Takasaki, Y; Wang, C; Xing, J; Ishizuka, K; Oya-Ito, T; Nakamura, Y; Arioka, Y; Maeda, T; Yamamoto, M; Yoshida, M; Noma, H; Hamada, S; Morikawa, M; Uno, Y; Okada, T; Iidaka, T; Iritani, S; Yamamoto, T; Miyashita, M; Kobori, A; Arai, M; Itokawa, M; Cheng, M-C; Chuang, Y-A; Chen, C-H; Suzuki, M; Takahashi, T; Hashimoto, R; Yamamori, H; Yasuda, Y; Watanabe, Y; Nunokawa, A; Someya, T; Ikeda, M; Toyota, T; Yoshikawa, T; Numata, S; Ohmori, T; Kunimoto, S; Mori, D; Iwata, N; Ozaki, N

    2017-03-01

    Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.

  9. A prebiotic, Celmanax™, decreases Escherichia coli O157:H7 colonization of bovine cells and feed-associated cytotoxicity in vitro

    Directory of Open Access Journals (Sweden)

    Juba Jean

    2011-04-01

    Full Text Available Abstract Background Escherichia coli O157:H7 is the most common serovar of enterohemorrhagic E. coli associated with serious human disease outbreaks. Cattle are the main reservoir with E. coli O157:H7 inducing hemorrhagic enteritis in persistent shedding beef cattle, however little is known about how this pathogen affects cattle health. Jejunal Hemorrhage Syndrome (JHS has unclear etiology but the pathology is similar to that described for E. coli O157:H7 challenged beef cattle suggestive that E. coli O157:H7 could be involved. There are no effective treatments for JHS however new approaches to managing pathogen issues in livestock using prebiotics and probiotics are gaining support. The first objective of the current study was to characterize pathogen colonization in hemorrhaged jejunum of dairy cattle during natural JHS outbreaks. The second objective was to confirm the association of mycotoxigenic fungi in feeds with the development of JHS and also to identify the presence of potential mycotoxins. The third objective was to determine the impact of a prebiotic, Celmanax™, or probiotic, Dairyman's Choice™ paste, on the cytotoxicity associated with feed extracts in vitro. The fourth objective was to determine the impact of a prebiotic or a probiotic on E. coli O157:H7 colonization of mucosal explants and a bovine colonic cell line in vitro. The final objective was to determine if prebiotic and probiotic feed additives could modify the symptoms that preceded JHS losses and the development of new JHS cases. Findings Dairy cattle developed JHS after consuming feed containing several types of mycotoxigenic fungi including Fusarium culmorum, F. poae, F. verticillioides, F. sporotrichioides, Aspergillusflavus, Penicillium roqueforti, P. crustosum, P. paneum and P. citrinum. Mixtures of Shiga toxin - producing Escherichia coli (STEC colonized the mucosa in the hemorrhaged tissues of the cattle and no other pathogen was identified. The STECs

  10. Modeling the contamination of lettuce with Escherichia coli 157:H7 from manure-amended soil and the effect of intervention strategies

    NARCIS (Netherlands)

    Franz, E.; Semenov, A.V.; Bruggen, van A.H.C.

    2008-01-01

    Aims: A growing number of foodborne illnesses has been associated with the consumption of fresh produce. In this study, the probability of lettuce contamination with Escherichia coli O157:H7 from manure-amended soil and the effect of intervention strategies was determined. Methods and Results:

  11. Heat shock and thermotolerance of Escherichia coli O157:H7 in a model beef gravy system and ground beef.

    Science.gov (United States)

    Juneja, V K; Klein, P G; Marmer, B S

    1998-04-01

    Duplicate beef gravy or ground beef samples inoculated with a suspension of a four-strain cocktail of Escherichia coli O157:H7 were subjected to sublethal heating at 46 degrees C for 15-30 min, and then heated to a final internal temperature of 60 degrees C. Survivor curves were fitted using a linear model that incorporated a lag period (TL), and D-values and 'time to a 4D inactivation' (T4D) were calculated. Heat-shocking allowed the organism to survive longer than non-heat-shocked cells; the T4D values at 60 degrees C increased 1.56- and 1.50-fold in beef gravy and ground beef, respectively. In ground beef stored at 4 degrees C, thermotolerance was lost after storage for 14 h. However, heat-shocked cells appeared to maintain their thermotolerance for at least 24 h in ground beef held to 15 or 28 degrees C. A 25 min heat shock at 46 degrees C in beef gravy resulted in an increase in the levels of two proteins with apparent molecular masses of 60 and 69 kDa. These two proteins were shown to be immunologically related to GroEL and DnaK, respectively. Increased heat resistance due to heat shock must be considered while designing thermal processes to assure the microbiological safety of thermally processed foods.

  12. Site-directed mutagenesis of Arg58 and Asp86 of elongation factor Tu from Escherichia coli: effects on the GTPase reaction and aminoacyl-tRNA binding

    DEFF Research Database (Denmark)

    Knudsen, Charlotte Rohde; Clark, Brian F. C.

    1996-01-01

    Elongation factor Tu from Escherichia coli was mutated separately at positions Asp86 and Arg58, in order to shed light both on the GTPase mechanism of elongation factor Tu and on the binding of aminoacyl-tRNA. In addition, the binding of guanine nucleotides was investigated by determination...

  13. Induction of genetic recombination in the lambda bacteriophage by ultraviolet radiation of the Escherichia Coli cells

    International Nuclear Information System (INIS)

    Alcantara D, D.

    1986-12-01

    In this work there are reported the results that show that although the stimulation of the recombination of the Lambda bacteriophage, by UV irradiation of the cells of Escherichia Coli, it looks to be the result of the high expression of the functions of the SOS system, doesn't keep some relationship with the high concentration of protein reached RecA. (Author)

  14. Gene Expression during Survival of Escherichia coli O157:H7 in Soil and Water

    Directory of Open Access Journals (Sweden)

    Ashley D. Duffitt

    2011-01-01

    Full Text Available The in vitro survival of Escherichia coli O157:H7 at 15∘C under two experimental conditions (sterile soil and sterile natural water was examined. DNA microarrays of the entire set of E. coli O157:H7 genes were used to measure the genomic expression patterns after 14 days. Although the populations declined, some E. coli O157:H7 cells survived in sterile stream water up to 234 days and in sterile soil for up to 179 days. Cells incubated in soil microcosms for 14 days expressed genes for antibiotic resistance, biosynthesis, DNA replication and modification, metabolism, phages, transposons, plasmids, pathogenesis and virulence, antibiotic resistance, ribosomal proteins, the stress response, transcription, translation, and transport and binding proteins at significantly higher levels than cells grown in Luria broth. These results suggest that E. coli O157:H7 may develop a different phenotype during transport through the environment. Furthermore, this pathogen may become more resistant to antibiotics making subsequent infections more difficult to treat.

  15. Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain.

    Directory of Open Access Journals (Sweden)

    Natalia Amigo

    Full Text Available Escherichia coli O157:H7 is responsible for severe diarrhea and hemolytic uremic syndrome (HUS, and predominantly affects children under 5 years. The major virulence traits are Shiga toxins, necessary to develop HUS and the Type III Secretion System (T3SS through which bacteria translocate effector proteins directly into the host cell. By SNPs typing, E. coli O157:H7 was separated into nine different clades. Clade 8 and clade 6 strains were more frequently associated with severe disease and HUS. In this study, we aimed to identify differentially expressed proteins in two strains of E. coli O157:H7 (clade 8 and clade 6, obtained from cattle and compared them with the well characterized reference EDL933 strain (clade 3. Clade 8 and clade 6 strains show enhanced pathogenicity in a mouse model and virulence-related properties. Proteins were extracted and analyzed using the TMT-6plex labeling strategy associated with two dimensional liquid chromatography and mass spectrometry in tandem. We detected 2241 proteins in the cell extract and 1787 proteins in the culture supernatants. Attention was focused on the proteins related to virulence, overexpressed in clade 6 and 8 strains compared to EDL933 strain. The proteins relevant overexpressed in clade 8 strain were the curli protein CsgC, a transcriptional activator (PchE, phage proteins, Stx2, FlgM and FlgD, a dienelactone hydrolase, CheW and CheY, and the SPATE protease EspP. For clade 6 strain, a high overexpression of phage proteins was detected, mostly from Stx2 encoding phage, including Stx2, flagellin and the protease TagA, EDL933_p0016, dienelactone hydrolase, and Haemolysin A, amongst others with unknown function. Some of these proteins were analyzed by RT-qPCR to corroborate the proteomic data. Clade 6 and clade 8 strains showed enhanced transcription of 10 out of 12 genes compared to EDL933. These results may provide new insights in E. coli O157:H7 mechanisms of pathogenesis.

  16. Inverse correlation between quasiparticle mass and T c in a cuprate high-T c superconductor.

    Science.gov (United States)

    Putzke, Carsten; Malone, Liam; Badoux, Sven; Vignolle, Baptiste; Vignolles, David; Tabis, Wojciech; Walmsley, Philip; Bird, Matthew; Hussey, Nigel E; Proust, Cyril; Carrington, Antony

    2016-03-01

    Close to a zero-temperature transition between ordered and disordered electronic phases, quantum fluctuations can lead to a strong enhancement of electron mass and to the emergence of competing phases such as superconductivity. A correlation between the existence of such a quantum phase transition and superconductivity is quite well established in some heavy fermion and iron-based superconductors, and there have been suggestions that high-temperature superconductivity in copper-oxide materials (cuprates) may also be driven by the same mechanism. Close to optimal doping, where the superconducting transition temperature T c is maximal in cuprates, two different phases are known to compete with superconductivity: a poorly understood pseudogap phase and a charge-ordered phase. Recent experiments have shown a strong increase in quasiparticle mass m* in the cuprate YBa2Cu3O7-δ as optimal doping is approached, suggesting that quantum fluctuations of the charge-ordered phase may be responsible for the high-T c superconductivity. We have tested the robustness of this correlation between m* and T c by performing quantum oscillation studies on the stoichiometric compound YBa2Cu4O8 under hydrostatic pressure. In contrast to the results for YBa2Cu3O7-δ, we find that in YBa2Cu4O8, the mass decreases as T c increases under pressure. This inverse correlation between m* and T c suggests that quantum fluctuations of the charge order enhance m* but do not enhance T c.

  17. A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number

    Science.gov (United States)

    Tadmor, Arbel

    2009-03-01

    In this work a biophysical model of Escherichia coli is presented that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steady-state growth, growing in a temporally and spatially constant environment, rich in resources. We apply this model to a series of past measurements, where the growth rate and rRNA-to-protein ratio have been measured for seven E. coli strains with an rRNA operon copy number ranging from one to seven (the wild-type copy number). These experiments show that growth rate markedly decreases for strains with fewer than six copies. Using the model, we were able to reproduce these measurements. We show that the model that best fits these data suggests that the volume fraction of macromolecules inside E. coli is not fixed when the rRNA operon copy number is varied. Moreover, the model predicts that increasing the copy number beyond seven results in a cytoplasm densely packed with ribosomes and proteins. Assuming that under such overcrowded conditions prolonged diffusion times tend to weaken binding affinities, the model predicts that growth rate will not increase substantially beyond the wild-type growth rate, as indicated by other experiments. Our model therefore suggests that changing the rRNA operon copy number of wild-type E. coli cells growing in a constant rich environment does not substantially increase their growth rate. Other observations regarding strains with an altered rRNA operon copy number, such as nucleoid compaction and the rRNA operon feedback response, appear to be qualitatively consistent with this model. In addition, we discuss possible design principles suggested by the model and propose further experiments to test its validity.

  18. Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog.

    Science.gov (United States)

    Herman, Daniel S; Smith, Christina; Liu, Chang; Vaughn, Cecily P; Palaniappan, Selvi; Pritchard, Colin C; Shirts, Brian H

    2018-07-01

    Detection of 3' PMS2 copy-number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequences using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges. The method was trained on 1352 samples, including 8 known positives, and tested on 719 samples, including 17 known positives. Clinical implementation of the first version of this method detected new mutations in the training (N = 7) and test (N = 2) sets that had not been identified by our initial clinical testing pipeline. The described final method showed complete sensitivity in both sample sets and false-positive rates of 5% (training) and 7% (test), dramatically decreasing the number of cases needing additional mutation evaluation. This approach leveraged the differences between gene and pseudogene to distinguish between PMS2 and PMS2CL copy-number mutations. These methods enable efficient and sensitive Lynch syndrome screening for 3' PMS2 copy-number mutations and may be applied similarly to other genomic regions with highly homologous pseudogenes. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  19. 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...

  20. Deteksi Produksi Toksin Stx-1 dan Stx-2 dari Escherichia coli O157:H7 Isolat Lokal Hasil Isolasi Feses dan Daging Sapi

    Directory of Open Access Journals (Sweden)

    I Wayan Suardana

    2009-12-01

    Full Text Available Shiga toxin produced by Escherichia coli O157:H7 can cause outbreaks and sporadic cases of serioushuman diseases. The diseases are indicated by hemorrhagic colitis and hemolytic uremic syndrome. Meatand meat products have been identified as vehicles of food borne disease caused by E.coli O157:H7. Themain aim of this research was to identify the correlation between the level of E.coli O157:H7 contaminationand the presence of Shiga toxin (Stx1 and Stx2 by applying method of Vero toxin Escherichia coli-ReversePassive Agglutination Test (VTEC-RPLA. The results showed that 3 of 7 isolates and 1 of 4 isolatesisolated from feces of cattle and beef, respectively produced Stx 1 (VT1. In the detection of Stx 2 (VT2, 4of 7 isolates and 1 of 4 isolates, isolated from the same samples were found to produce this toxin.According to all isolates, in this research showed, 1 isolate was found to produce VT2, 4 isolates to produceboth VT1 and VT2, while 6 isolates showed negative results either to VT1 or VT2.

  1. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

    Directory of Open Access Journals (Sweden)

    Victor Renault

    Full Text Available Copy number variations (CNV include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information.To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer, a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs Affymetrix SNP Array data (Fig 1A. Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test, validated by another cohort of HCCs (p-value of 5.6e-7 (Fig 2B.aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/.aCNViewer@cephb.fr.

  2. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

    Science.gov (United States)

    Renault, Victor; Tost, Jörg; Pichon, Fabien; Wang-Renault, Shu-Fang; Letouzé, Eric; Imbeaud, Sandrine; Zucman-Rossi, Jessica; Deleuze, Jean-François; How-Kit, Alexandre

    2017-01-01

    Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https

  3. HPV16-E7-Specific Activated CD8 T Cells in E7 Transgenic Skin and Skin Grafts

    Directory of Open Access Journals (Sweden)

    Seyed Davoud Jazayeri

    2017-05-01

    Full Text Available Human papillomavirus (HPV 16 E7 (E7 protein expression in skin promotes epithelial hyperproliferation and transformation to malignancy. Grafts of murine skin expressing E7 protein as a transgene in keratinocytes are not rejected from immunocompetent recipients, whereas grafts expressing ovalbumin (OVA, with or without coexpression of E7 protein, are promptly rejected, demonstrating that E7-associated non-antigen-specific local immunosuppression is not a major determinant of lack of rejection of E7 transgenic skin. To determine whether failure of rejection of E7 skin grafts is due to failure to attract E7-specific effector T cells, E7- and OVA-specific effector CD8+ T cells, activated in vitro, were transferred to animals bearing E7 transgenic skin grafts. Three days after T cell transfer, E7-specific T cells were present in significantly greater numbers than OVA-specific T cells in the grafted skin on animals bearing recently placed or healed E7 grafts, without graft rejection, and also in the ear skin of E7 transgenic animals, without obvious pathology. E7 and OVA-specific T cells were present in lesser numbers in healed E7 grafts than in recently placed grafts and in lesser numbers in recently placed E7 transgenic epidermal grafts without E7-associated hyperproliferation, derived from E7 transgenic mice with a mutated retinoblastoma gene. These data demonstrate that effector T cells are to some extent attracted to E7 transgenic skin specifically by E7 expression, but in large measure non-specifically by the epithelial proliferation associated with E7 expression, and by the local inflammation produced by grafting. Failure of E7 graft rejection was observed despite trafficking of E7-specific effector T cells to E7-expressing epithelium, a finding of consequence for immunotherapy of HPV 16 E7-associated human cancers.

  4. Morphological imaging and T2 and T2* mapping of hip cartilage at 7 Tesla MRI under the influence of intravenous gadolinium

    International Nuclear Information System (INIS)

    Lazik-Palm, Andrea; Geis, Christina; Goebel, Juliane; Theysohn, Jens M.; Kraff, Oliver; Johst, Soeren; Ladd, Mark E.; Quick, Harald H.

    2016-01-01

    To investigate the influence of intravenous gadolinium on cartilage T2 and T2* relaxation times and on morphological image quality at 7-T hip MRI. Hips of 11 healthy volunteers were examined at 7 T. Multi-echo sequences for T2 and T2* mapping, 3D T1 volumetric interpolated breath-hold examination (VIBE) and double-echo steady-state (DESS) sequences were acquired before and after intravenous application of gadolinium according to a delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) protocol. Cartilage relaxation times were measured in both scans. Morphological sequences were assessed quantitatively using contrast ratios and qualitatively using a 4-point Likert scale. Student's t-test, Pearson's correlation (ρ) and Wilcoxon sign-rank test were used for statistical comparisons. Pre- and post-contrast T2 and T2* values were highly correlated (T2: acetabular: ρ = 0.76, femoral: ρ = 0.77; T2*: acetabular: ρ = 0.80, femoral: ρ = 0.72). Gadolinium enhanced contrasts between cartilage and joint fluid in DESS and T1 VIBE according to the qualitative (p = 0.01) and quantitative (p < 0.001) analysis. The delineation of acetabular and femoral cartilage and the labrum predominantly improved with gadolinium. Gadolinium showed no relevant influence on T2 or T2* relaxation times and improved morphological image quality at 7 T. Therefore, morphological and quantitative sequences including dGEMRIC can be conducted in a one-stop-shop examination. (orig.)

  5. Morphological imaging and T2 and T2* mapping of hip cartilage at 7 Tesla MRI under the influence of intravenous gadolinium

    Energy Technology Data Exchange (ETDEWEB)

    Lazik-Palm, Andrea; Geis, Christina; Goebel, Juliane; Theysohn, Jens M. [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Kraff, Oliver; Johst, Soeren [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); Ladd, Mark E. [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); German Cancer Research Center (DKFZ), Division of Medical Physics in Radiology, Heidelberg (Germany); Quick, Harald H. [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); University Hospital Essen, High-Field and Hybrid MR Imaging, Essen (Germany)

    2016-11-15

    To investigate the influence of intravenous gadolinium on cartilage T2 and T2* relaxation times and on morphological image quality at 7-T hip MRI. Hips of 11 healthy volunteers were examined at 7 T. Multi-echo sequences for T2 and T2* mapping, 3D T1 volumetric interpolated breath-hold examination (VIBE) and double-echo steady-state (DESS) sequences were acquired before and after intravenous application of gadolinium according to a delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) protocol. Cartilage relaxation times were measured in both scans. Morphological sequences were assessed quantitatively using contrast ratios and qualitatively using a 4-point Likert scale. Student's t-test, Pearson's correlation (ρ) and Wilcoxon sign-rank test were used for statistical comparisons. Pre- and post-contrast T2 and T2* values were highly correlated (T2: acetabular: ρ = 0.76, femoral: ρ = 0.77; T2*: acetabular: ρ = 0.80, femoral: ρ = 0.72). Gadolinium enhanced contrasts between cartilage and joint fluid in DESS and T1 VIBE according to the qualitative (p = 0.01) and quantitative (p < 0.001) analysis. The delineation of acetabular and femoral cartilage and the labrum predominantly improved with gadolinium. Gadolinium showed no relevant influence on T2 or T2* relaxation times and improved morphological image quality at 7 T. Therefore, morphological and quantitative sequences including dGEMRIC can be conducted in a one-stop-shop examination. (orig.)

  6. Production of D-tagatose at high temperatures using immobilized Escherichia coli cells expressing L-arabinose isomerase from Thermotoga neapolitana.

    Science.gov (United States)

    Hong, Young-Ho; Lee, Dong-Woo; Lee, Sang-Jae; Choe, Eun-Ah; Kim, Seong-Bo; Lee, Yoon-Hee; Cheigh, Chan-Ick; Pyun, Yu-Ryang

    2007-04-01

    Escherichia coli cells expressing L-arabinose isomerase from Thermotoga neapolitana (TNAI) were immobilized in calcium alginate beads. The resulting cell reactor (2.4 U, t (1/2) = 43 days at 70 degrees C) in a continuous recycling mode at 70 degrees C produced 49 and 38 g D-tagatose/l from 180 and 90 g D-galactose/l, respectively, within 12 h.

  7. Two tandem RNase III cleavage sites determine betT mRNA stability in response to osmotic stress in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Minji Sim

    Full Text Available While identifying genes regulated by ribonuclease III (RNase III in Escherichia coli, we observed that steady-state levels of betT mRNA, which encodes a transporter mediating the influx of choline, are dependent on cellular concentrations of RNase III. In the present study, we also observed that steady-state levels of betT mRNA are dependent on RNase III activity upon exposure to osmotic stress, indicating the presence of cis-acting elements controlled by RNase III in betT mRNA. Primer extension analyses of betT mRNA revealed two tandem RNase III cleavage sites in its stem-loop region, which were biochemically confirmed via in vitro cleavage assays. Analyses of cleavage sites suggested the stochastic selection of cleavage sites by RNase III, and mutational analyses indicated that RNase III cleavage at either site individually is insufficient for efficient betT mRNA degradation. In addition, both the half-life and abundance of betT mRNA were significantly increased in association with decreased RNase III activity under hyper-osmotic stress conditions. Our findings demonstrate that betT mRNA stability is controlled by RNase III at the post-transcriptional level under conditions of osmotic stress.

  8. Screening for common copy-number variants in cancer genes.

    Science.gov (United States)

    Tyson, Jess; Majerus, Tamsin M O; Walker, Susan; Armour, John A L

    2010-12-01

    For most cases of colorectal cancer that arise without a family history of the disease, it is proposed that an appreciable heritable component of predisposition is the result of contributions from many loci. Although progress has been made in identifying single nucleotide variants associated with colorectal cancer risk, the involvement of low-penetrance copy number variants is relatively unexplored. We have used multiplex amplifiable probe hybridization (MAPH) in a fourfold multiplex (QuadMAPH), positioned at an average resolution of one probe per 2 kb, to screen a total of 1.56 Mb of genomic DNA for copy number variants around the genes APC, AXIN1, BRCA1, BRCA2, CTNNB1, HRAS, MLH1, MSH2, and TP53. Two deletion events were detected, one upstream of MLH1 in a control individual and the other in APC in a colorectal cancer patient, but these do not seem to correspond to copy number polymorphisms with measurably high population frequencies. In summary, by means of our QuadMAPH assay, copy number measurement data were of sufficient resolution and accuracy to detect any copy number variants with high probability. However, this study has demonstrated a very low incidence of deletion and duplication variants within intronic and flanking regions of these nine genes, in both control individuals and colorectal cancer patients. Copyright © 2010 Elsevier Inc. All rights reserved.

  9. Effects of high hydrostatic pressure and temperature increase on Escherichia coli spp. and pectin methyl esterase inactivation in orange juice.

    Science.gov (United States)

    Torres, E F; González-M, G; Klotz, B; Rodrigo, D

    2016-03-01

    The aim of this study was to evaluate the effect of high hydrostatic pressure treatment combined with moderate processing temperatures (25 ℃-50 ℃) on the inactivation of Escherichia coli O157: H7 (ATCC 700728), E. coli K12 (ATCC 23716), and pectin methyl esterase in orange juice, using pressures of 250 to 500 MPa with times ranging between 1 and 30 min. Loss of viability of E. coli O157:H7 increased significantly as pressure and treatment time increased, achieving a 6.5 log cycle reduction at 400 MPa for 3 min at 25 ℃ of treatment. With regard to the inactivation of pectin methyl esterase, the greatest reduction obtained was 90.05 ± 0.01% at 50 ℃ and 500 MPa of pressure for 15 min; therefore, the pectin methyl esterase enzyme was highly resistant to the treatments by high hydrostatic pressure. The results obtained in this study showed a synergistic effect between the high pressure and moderate temperatures in inactivating E. coli cells. © The Author(s) 2016.

  10. Growth of Escherichia coli O157:H7, Non-O157 Shiga Toxin-Producing Escherichia coli , and Salmonella in Water and Hydroponic Fertilizer Solutions.

    Science.gov (United States)

    Shaw, Angela; Helterbran, Kara; Evans, Michael R; Currey, Christopher

    2016-12-01

    The desire for local, fresh produce year round is driving the growth of hydroponic growing systems in the United States. Many food crops, such as leafy greens and culinary herbs, grown within hydroponics systems have their root systems submerged in recirculating nutrient-dense fertilizer solutions from planting through harvest. If a foodborne pathogen were introduced into this water system, the risk of contamination to the entire crop would be high. Hence, this study was designed to determine whether Escherichia coli O157:H7, non-O157 Shiga toxin-producing E. coli , and Salmonella were able to survive and reproduce in two common hydroponic fertilizer solutions and in water or whether the bacteria would be killed or suppressed by the fertilizer solutions. All the pathogens grew by 1 to 6 log CFU/ml over a 24-h period, depending on the solution. E. coli O157:H7 reached higher levels in the fertilizer solution with plants (3.12 log CFU/ml), whereas non-O157 Shiga toxin-producing E. coli and Salmonella reached higher levels in the fertilizer solution without plants (1.36 to 3.77 log CFU/ml). The foodborne pathogens evaluated here survived for 24 h in the fertilizer solution, and populations grew more rapidly in these solutions than in plain water. Therefore, human pathogens entering the fertilizer solution tanks in hydroponic systems would be expected to rapidly propagate and spread throughout the system and potentially contaminate the entire crop.

  11. Bovine milk fat globule membrane affects virulence expression in Escherichia coli O157:H7.

    Science.gov (United States)

    Tellez, A; Corredig, M; Guri, A; Zanabria, R; Griffiths, M W; Delcenserie, V

    2012-11-01

    The aim of this study was to examine the effect of the bovine milk fat globule membrane (MFGM) on the virulence of Escherichia coli O157:H7. The MFGM was extracted from raw or heat-treated milk, resulting in 2 preparations differing in protein composition. Both heated and raw MFGM exerted an inhibitory effect on Shiga toxin gene expression by E. coli O157:H7 (ratios of -7.69 and -5.96, respectively). Interestingly, the effect was stronger with heated MFGM, with a larger decrease in expression of the virulence gene fliC (ratio of -9.43). The difference in effect observed between heated and raw MFGM could be explained by the difference in protein composition between the 2 preparations. These results show, for the first time, a specific effect of MFGM on expressionof Shiga toxin genes as well as genes involved in the motility of E. coli O157:H7. This may offer a new approach to mitigate the adverse health effects caused by E. coli O157:H7 infections. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. Copying of holograms by spot scanning approach.

    Science.gov (United States)

    Okui, Makoto; Wakunami, Koki; Oi, Ryutaro; Ichihashi, Yasuyuki; Jackin, Boaz Jessie; Yamamoto, Kenji

    2018-05-20

    To replicate holograms, contact copying has conventionally been used. In this approach, a photosensitive material is fixed together with a master hologram and illuminated with a coherent beam. This method is simple and enables high-quality copies; however, it requires a large optical setup for large-area holograms. In this paper, we present a new method of replicating holograms that uses a relatively compact optical system even for the replication of large holograms. A small laser spot that irradiates only part of the hologram is used to reproduce the hologram by scanning the spot over the whole area of the hologram. We report on the results of experiments carried out to confirm the copy quality, along with a guide to design scanning conditions. The results show the potential effectiveness of the large-area hologram replication technology using a relatively compact apparatus.

  13. Quantitative Microbial Risk Assessment for Escherichia coli O157:H7 in Fresh-Cut Lettuce.

    Science.gov (United States)

    Pang, Hao; Lambertini, Elisabetta; Buchanan, Robert L; Schaffner, Donald W; Pradhan, Abani K

    2017-02-01

    Leafy green vegetables, including lettuce, are recognized as potential vehicles for foodborne pathogens such as Escherichia coli O157:H7. Fresh-cut lettuce is potentially at high risk of causing foodborne illnesses, as it is generally consumed without cooking. Quantitative microbial risk assessments (QMRAs) are gaining more attention as an effective tool to assess and control potential risks associated with foodborne pathogens. This study developed a QMRA model for E. coli O157:H7 in fresh-cut lettuce and evaluated the effects of different potential intervention strategies on the reduction of public health risks. The fresh-cut lettuce production and supply chain was modeled from field production, with both irrigation water and soil as initial contamination sources, to consumption at home. The baseline model (with no interventions) predicted a mean probability of 1 illness per 10 million servings and a mean of 2,160 illness cases per year in the United States. All intervention strategies evaluated (chlorine, ultrasound and organic acid, irradiation, bacteriophage, and consumer washing) significantly reduced the estimated mean number of illness cases when compared with the baseline model prediction (from 11.4- to 17.9-fold reduction). Sensitivity analyses indicated that retail and home storage temperature were the most important factors affecting the predicted number of illness cases. The developed QMRA model provided a framework for estimating risk associated with consumption of E. coli O157:H7-contaminated fresh-cut lettuce and can guide the evaluation and development of intervention strategies aimed at reducing such risk.

  14. A Newly Emergent Turkey Arthritis Reovirus Shows Dominant Enteric Tropism and Induces Significantly Elevated Innate Antiviral and T Helper-1 Cytokine Responses.

    Directory of Open Access Journals (Sweden)

    Tamer A Sharafeldin

    Full Text Available Newly emergent turkey arthritis reoviruses (TARV were isolated from tendons of lame 15-week-old tom turkeys that occasionally had ruptured leg tendons. Experimentally, these TARVs induced remarkable tenosynovitis in gastrocnemius tendons of turkey poults. The current study aimed to characterize the location and the extent of virus replication as well as the cytokine response induced by TARV during the first two weeks of infection. One-week-old male turkeys were inoculated orally with TARV (O'Neil strain. Copy numbers of viral genes were estimated in intestines, internal organs and tendons at ½, 1, 2, 3, 4, 7, 14 days Post inoculation (dpi. Cytokine profile was measured in intestines, spleen and leg tendons at 0, 4, 7 and 14 dpi. Viral copy number peaked in jejunum, cecum and bursa of Fabricius at 4 dpi. Copy numbers increased dramatically in leg tendons at 7 and 14 dpi while minimal copies were detected in internal organs and blood during the same period. Virus was detected in cloacal swabs at 1-2 dpi, and peaked at 14 dpi indicating enterotropism of the virus and its early shedding in feces. Elevation of IFN-α and IFN-β was observed in intestines at 7 dpi as well as a prominent T helper-1 response (IFN-γ at 7 and 14 dpi. IFN-γ and IL-6 were elevated in gastrocnemius tendons at 14 dpi. Elevation of antiviral cytokines in intestines occurred at 7dpi when a significant decline of viral replication in intestines was observed. T helper-1 response in intestines and leg tendons was the dominant T-helper response. These results suggest the possible correlation between viral replication and cytokine response in early infection of TARV in turkeys. Our findings provide novel insights which help elucidate viral pathogenesis in turkey tendons infected with TARV.

  15. Nano Polyamidoamine-G7 (NPAMAM-G7 Dendrimer Synthesis and Assessment the Effect of its antibacterial on Escherichia Coli, Klebsiella Oxytoca, Pseudomonas Aeruginosa , Proteus Mirabilis and Staphylococcus Aureus from aqueous solution

    Directory of Open Access Journals (Sweden)

    mitra Gholami

    2016-06-01

    Full Text Available Background: Nano scale dendrimers are macromolecules synthetic which frequently used in medical and health field. This study was aimed to examine synthesis and the antibacterial effect of NanoPolyamidoamine-G7 (NPAMAM-G7 dendrimer on Escherichia Coli, Klebsiella Oxytoca, Pseudomonas Aeruginosa , Proteus Mirabilis and Staphylococcus Aureus from aqueous solution. Material and methods: In this experimental study, initially dilution of 103 CFU/ml were prepared from each strain of bacteria. Then different concentrations of dendrimer (0.025, 0.25, 2.5 and 25 µg/ml in the laboratory temperature (23-25 °C was added to water. In order to determine the efficiency of dendrimers in removal of bacteria, samples were taken at different times (0, 10, 20, 30, 40, 50 and 60 min and were cultured on nutrient agar medium. Samples were incubated for 24 hours at 37 °C and then number of colonies were counted. Results: Antibacterial properties of dendrimers in aqueous solution by increasing the dendrimer concentration and contact time is directly related. At a concentration of 25 μg/ml at 60 minutes all bacteria except Staphylococcus Aureus, and at 30 minutes, Escherichia Coli and Klebsiella Oxytoca bacteria for 100% excluded. The concentration of 2.5 μg/ml at 60 minutes of bacteria, Escherichia Coli, Klebsiella Oxytoca and Proteus Mirabilis are 100% excluded. All concentrations of dendrimers at different times were reduced bacteria in the PAMAM- G7 dendrimer effect on gram-negative bacteria, gram-positive bacteria was better. Conclusion: The NPAMAM-G7 dendrimer with end amine groups exhibited a positive impact on the removal of standard strains, gram-positive and gram-negative bacteria. Therefore, it is possible to use these nanodendrimers as antibacterial in the future.

  16. FBXW7 and NOTCH1 mutations in childhood T cell acute lymphoblastic leukaemia and T cell non-Hodgkin lymphoma.

    Science.gov (United States)

    Park, Myoung-Ja; Taki, Tomohiko; Oda, Megumi; Watanabe, Tomoyuki; Yumura-Yagi, Keiko; Kobayashi, Ryoji; Suzuki, Nobuhiro; Hara, Junichi; Horibe, Keizo; Hayashi, Yasuhide

    2009-04-01

    Mutation analysis of FBXW7 and NOTCH1 genes was performed in 55 T cell acute lymphoblastic leukaemia (T-ALL) and 14 T cell non-Hodgkin lymphoma (T-NHL) patients who were treated on the Japan Association of Childhood Leukaemia Study (JACLS) protocols ALL-97 and NHL-98. FBXW7 and/or NOTCH1 mutations were found in 22 (40.0%) of 55 T-ALL and 7 (50.0%) of 14 T-NHL patients. FBXW7 mutations were found in 8 (14.6%) of 55 T-ALL and 3 (21.4%) of 14 T-NHL patients, and NOTCH1 mutations in 17 (30.9%) of 55 T-ALL and 6 (42.9%) of 14 T-NHL patients. Three (5.4%) T-ALL and two (1.4%) T-NHL patients had mutations in both FBXW7 and NOTCH1. FBXW7 mutations included one insertion, one deletion, one deletion/insertion and nine missense mutations. NOTCH1 mutations were detected in the heterodimerization domain (HD) in 15 cases, in the PEST domain in seven cases, and in both the HD and PEST domains in one case. Five-year event-free survival and overall survival for patients with FBXW7 and/or NOTCH1 mutations were 95.5% (95% CI, 71.9-99.4%) and 100% respectively, suggesting that T-ALL patients with FBXW7 and/or NOTCH1 mutation represent a good prognosis compared to those without FBXW7 and/or NOTCH1 mutations (63.6%, P = 0.007 and 78.8%, P = 0.023, respectively).

  17. Helicase and Polymerase Move Together Close to the Fork Junction and Copy DNA in One-Nucleotide Steps

    Directory of Open Access Journals (Sweden)

    Manjula Pandey

    2014-03-01

    Full Text Available By simultaneously measuring DNA synthesis and dNTP hydrolysis, we show that T7 DNA polymerase and T7 gp4 helicase move in sync during leading-strand synthesis, taking one-nucleotide steps and hydrolyzing one dNTP per base-pair unwound/copied. The cooperative catalysis enables the helicase and polymerase to move at a uniformly fast rate without guanine:cytosine (GC dependency or idling with futile NTP hydrolysis. We show that the helicase and polymerase are located close to the replication fork junction. This architecture enables the polymerase to use its strand-displacement synthesis to increase the unwinding rate, whereas the helicase aids this process by translocating along single-stranded DNA and trapping the unwound bases. Thus, in contrast to the helicase-only unwinding model, our results suggest a model in which the helicase and polymerase are moving in one-nucleotide steps, DNA synthesis drives fork unwinding, and a role of the helicase is to trap the unwound bases and prevent DNA reannealing.

  18. Chimpanzees copy dominant and knowledgeable individuals: implications for cultural diversity.

    Science.gov (United States)

    Kendal, Rachel; Hopper, Lydia M; Whiten, Andrew; Brosnan, Sarah F; Lambeth, Susan P; Schapiro, Steven J; Hoppitt, Will

    2015-01-01

    Evolutionary theory predicts that natural selection will fashion cognitive biases to guide when, and from whom, individuals acquire social information, but the precise nature of these biases, especially in ecologically valid group contexts, remains unknown. We exposed four captive groups of chimpanzees ( Pan troglodytes ) to a novel extractive foraging device and, by fitting statistical models, isolated four simultaneously operating transmission biases. These include biases to copy (i) higher-ranking and (ii) expert individuals, and to copy others when (iii) uncertain or (iv) of low rank. High-ranking individuals were relatively un-strategic in their use of acquired knowledge, which, combined with the bias for others to observe them, may explain reports that high innovation rates (in juveniles and subordinates) do not generate a correspondingly high frequency of traditions in chimpanzees. Given the typically low rank of immigrants in chimpanzees, a 'copying dominants' bias may contribute to the observed maintenance of distinct cultural repertoires in neighboring communities despite sharing similar ecology and knowledgeable migrants. Thus, a copying dominants strategy may, as often proposed for conformist transmission, and perhaps in concert with it, restrict the accumulation of traditions within chimpanzee communities whilst maintaining cultural diversity.

  19. Inactivation of Escherichia coli O157:H7, salmonellae, and Campylobacter jejuni in raw ground beef by gamma irradiation

    International Nuclear Information System (INIS)

    Clavero, M.R.S.; Monk, J.D.; Beuchat, L.R.; Doyle, M.P.; Brackett, R.E.

    1994-01-01

    Raw ground beef patties inoculated with stationary-phase cells of Escherichia coli O157:H7, salmonellae, or Campylobacter jejuni were subjected to gamma irradiation (60Co) treatment, with doses ranging from 0 to 2.52 kGy. The influence of two levels of fat (8 to 14% [low fat] and 27 to 28% [high fat]) and temperature (frozen [-17 to -15 degrees C] and refrigerated [3 to 5 degrees C]) on the inactivation of each pathogen by irradiation was investigated. In ascending order of irradiation resistance, the D10 values ranged from 0.175 to 0.235 kGy (C. jejuni), from 0.241 to 0.307 kGy (E. coli O157:H7), and from 0.618 to 0.800 kGy (salmonellae). Statistical analysis revealed that E. coli O157:H7 had a significantly (P 0.05) higher D10 value when irradiated at -17 to -15 degrees C than when irradiated at 3 to 5 degrees C. Regardless of the temperature during irradiation, the level of fat did not have a significant effect on the D10 value. Salmonellae behaved like E. coli O157:H7 in low-fat beef, but temperature did not have a significant effect when the pathogen was irradiated in high-fat ground beef. Significantly higher D10 values were calculated for C. jejuni irradiated in frozen than in refrigerated low-fat beef. C. jejuni was more resistant to irradiation in low-fat beef than in high-fat beef when treatment was at -17 to -15 degrees C. Regardless of the fat level and temperature during inactivation, these pathogens were highly sensitive to gamma irradiation. An applied dose of 2.5 kGy would be sufficient to kill 10(8.1) E. coli O157:H7, 10(3.1) salmonellae, and 10(10.6) C. jejuni, resulting in a high probability of complete inactivation of populations much higher than those occasionally present in ground beef patties

  20. A Specialized Multi-Transmit Head Coil for High Resolution fMRI of the Human Visual Cortex at 7T.

    Science.gov (United States)

    Sengupta, Shubharthi; Roebroeck, Alard; Kemper, Valentin G; Poser, Benedikt A; Zimmermann, Jan; Goebel, Rainer; Adriany, Gregor

    2016-01-01

    To design, construct and validate radiofrequency (RF) transmit and receive phased array coils for high-resolution visual cortex imaging at 7 Tesla. A 4 channel transmit and 16 channel receive array was constructed on a conformal polycarbonate former. Transmit field efficiency and homogeneity were simulated and validated, along with the Specific Absorption Rate, using [Formula: see text] mapping techniques and electromagnetic simulations. Receiver signal-to-noise ratio (SNR), temporal SNR (tSNR) across EPI time series, g-factors for accelerated imaging and noise correlations were evaluated and compared with a commercial 32 channel whole head coil. The performance of the coil was further evaluated with human subjects through functional MRI (fMRI) studies at standard and submillimeter resolutions of upto 0.8mm isotropic. The transmit and receive sections were characterized using bench tests and showed good interelement decoupling, preamplifier decoupling and sample loading. SNR for the 16 channel coil was ∼ 1.5 times that of the commercial coil in the human occipital lobe, and showed better g-factor values for accelerated imaging. fMRI tests conducted showed better response to Blood Oxygen Level Dependent (BOLD) activation, at resolutions of 1.2mm and 0.8mm isotropic. The 4 channel phased array transmit coil provides homogeneous excitation across the visual cortex, which, in combination with the dual row 16 channel receive array, makes for a valuable research tool for high resolution anatomical and functional imaging of the visual cortex at 7T.

  1. A stable CC-chemokine receptor (CCR)-5 tropic virus is correlated with the persistence of HIV RNA at less than 2.5 copies in successfully treated naïve subjects.

    Science.gov (United States)

    Parisi, Saverio Giuseppe; Andreis, Samantha; Mengoli, Carlo; Scaggiante, Renzo; Cruciani, Mario; Ferretto, Roberto; Manfrin, Vinicio; Panese, Sandro; Basso, Monica; Boldrin, Caterina; Bressan, Stefania; Sarmati, Loredana; Andreoni, Massimo; Palù, Giorgio

    2013-07-11

    To determine if tropism for CXCR4 or CCR5 correlates with cellular HIV DNA load, residual viraemia and CD4 count in 219 successfully treated naive subjects with HIV infection enrolled in five infectious diseases units in Northeastern Italy. A subset of subjects, achieving plasma HIV RNA level <50 copies/ml after initiation of first-line therapy and maintaining it until follow-up time points, was retrospectively selected from a prospective cohort. Blood samples were collected before the beginning of therapy (T0), at the first follow-up time (T1) and, when available, at a second (T2) follow-up time. HIV DNA, CD4 count and plasma viraemia were available from all 219 patients at T0 and T1, and in 86 subjects at T2, while tropism determinations were available from 109 subjects at T0, 219 at T1, and from 86 subjects at T2. Achieving residual viraemia <2.5 copies/ml at T1 correlated with having the same condition at T2 (p = 0.0007). X4 tropism at T1 was negatively correlated with the possibility of achieving viraemia<2.5 copies/ml at T2 (p = 0.0076). T1-T2 tropism stability was significant (p <0.0001). T0 tropism correlated with T1 and T2 tropism (p < 0.001); therefore the stability of the tropism over the two follow-up periods was significant (p = 0.0003). An effective viremic suppression (viraemia<2.5 copies/ml) correlated with R5 coreceptor affinity (p= 0.047). The tropism of archived virus was stable during an effective treatment, with 15-18% of subjects switching over time, despite a viraemia<50 copies/ml. R5 tropism and its stability were related to achieving and maintaining viraemia<2.5 copies/ml.

  2. 4-thiouridine and photoprotection in Escherichia coli K12

    International Nuclear Information System (INIS)

    Thomas, Gilles; Favre, Alain

    1977-01-01

    A high level of protection is observed in the Escherichia coli K 12 strain AB 1157 rec A 1 nuv + whose transfer RNA contains 4-thiouridine. In contrast, the photoprotection level is low and observed at higher doses in a strain which differs from the former by a single mutation nuv - , (lack of 4-thiouridine). This nucleoside is therefore an important chromophore leading to photoprotection. This conclusion is corroborated by the similarity of the action spectra for 8-13 link formation in tRNA and for photoprotection [fr

  3. Elimination of Escherichia coli O157:H7 in meats by gamma irradiation

    International Nuclear Information System (INIS)

    Thayer, D.W.; Boyd, G.

    1993-01-01

    Undercooked and raw meat has been linked to outbreaks of hemorrhagic diarrhea due to the presence of Escherichia coli O157:H7; therefore, treatment with ionizing radiation was investigated as a potential method for the elimination of this organism. Response-surface methods were used to study the effects of irradiation dose (0 to 2.0 kGy), temperature (-20 to +20 degrees C), and atmosphere (air and vacuum) on E. coli O157:H7 in mechanically deboned chicken meat. Differences in irradiation dose and temperature significantly affected the results. Ninety percent of the viable E. coli in chicken meat was eliminated by doses of 0.27 kGy at +5 degrees C and 0.42 kGy at -5 degrees C. Small, but significant, differences in radiation resistance by E. coli were found when finely ground lean beef rather than chicken was the substrate. Unlike nonirradiated samples, no measurable verotoxin was found in finely ground lean beef which had been inoculated with 10(4.8) CFU of E. coli O157:H7 per g, irradiated at a minimum dose of 1.5 kGy, and temperature abused at 35 degrees C for 20 h. Irradiation is an effective method to control this food-borne pathogen

  4. Visualized and precise design of artificial small RNAs for regulating T7 RNA polymerase and enhancing recombinant protein folding in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Yujia Zhao

    2016-12-01

    Full Text Available Small non-coding RNAs (sRNAs have received much attention in recent years due to their unique biological properties, which can efficiently and specifically tune target gene expressions in bacteria. Inspired by natural sRNAs, recent works have proposed the use of artificial sRNAs (asRNAs as genetic tools to regulate desired gene that has been applied in several fields, such as metabolic engineering and bacterial physiology studies. However, the rational design of asRNAs is still a challenge. In this study, we proposed structure and length as two criteria to implement rational visualized and precise design of asRNAs. T7 expression system was one of the most useful recombinant protein expression systems. However, it was deeply limited by the formation of inclusion body. To settle this problem, we designed a series of asRNAs to inhibit the T7 RNA polymerase (Gene1 expression to balance the rate between transcription and folding of recombinant protein. Based on the heterologous expression of Aspergillus oryzae Li-3 glucuronidase in E. coli, the asRNA-antigene1-17bp can effectively decrease the inclusion body and increase the enzyme activity by 169.9%.

  5. Recombinant cholera toxin B subunit in Escherichia coli: high-level secretion, purification, and characterization

    NARCIS (Netherlands)

    Slos, P.; Speck, D.; Accart, N.; Kolbe, H.V.; Schubnel, D.; Bouchon, B.; Bischoff, Rainer; Kieny, M.P.

    1994-01-01

    The gene coding for cholera toxin subunit B (CT-B) was fused to a modified ompA signal sequence and subsequently cloned into a high expression vector based on the regulatory signals of the arabinose operon of Salmonella typhimurium. Upon induction of gene expression in Escherichia coli, a product of

  6. [Relationship between mitochondrial DNA copy number, membrane potential of human embryo and embryo morphology].

    Science.gov (United States)

    Zhao, H; Teng, X M; Li, Y F

    2017-11-25

    Objective: To explore the relationship between the embryo with the different morphological types in the third day and its mitochondrial copy number, the membrane potential. Methods: Totally 117 embryos with poor development after normal fertilization and were not suitable transferred in the fresh cycle and 106 frozen embryos that were discarded voluntarily by infertility patients with in vitro fertilization-embryo transfer after successful pregnancy were selected. According to evaluation of international standard in embryos, all cleavage stage embryos were divided into class Ⅰ frozen embryo group ( n= 64), class Ⅱ frozen embryo group ( n= 42) and class Ⅲ fresh embryonic group (not transplanted embryos; n= 117). Real-time PCR and confocal microscopy methods were used to detect mitochondrial DNA (mtDNA) copy number and the mitochondrial membrane potential of a single embryo. The differences between embryo quality and mtDNA copy number and membrane potential of each group were compared. Results: The copy number of mtDNA and the mitochondrial membrane potential in class Ⅲ fresh embryonic group [(1.7±1.0)×10(5) copy/μl, 1.56±0.32] were significantly lower than those in class Ⅰ frozen embryo group [(3.4±1.7)×10(5) copy/μl, 2.66±0.21] and class Ⅱ frozen embryo group [(2.6±1.2)×10(5) copy/μl, 1.80±0.32; all Pembryo group were significantly higher than those in classⅡ frozen embryo group (both Pembryos of the better quality embryo are higher.

  7. Meat Science and Muscle Biology Symposium: Escherichia coli O157:H7, diet, and fecal microbiome in beef cattle.

    Science.gov (United States)

    Wells, J E; Kim, M; Bono, J L; Kuehn, L A; Benson, A K

    2014-04-01

    Shiga-toxigenic Escherichia coli, such as E. coli O157:H7, are foodborne zoonotic pathogens that can cause severe illness and death in humans. The gastrointestinal tract of ruminant animals has been identified as a primary habitat for E. coli O157:H7 and, in cattle, the hindgut tract appears to be a primary site for colonization. This pathogen has been found in cattle feces, on cattle hides, and in the production environment, and transmission to humans has occurred as a result of consumption of contaminated ground beef, water, and produce. Interventions to reduce the pathogen at beef harvest have significantly reduced the occurrence of the pathogen, but outbreaks and recalls due to the pathogen still occur for beef products. Interventions in the feedyard before harvest have had little success, but critical control points for implementing interventions are limited compared with the beef abattoir. The percentage of animals shedding E. coli O157:H7 in the feces can be highly variable from pen to pen, and the levels in the feces can vary from animal to animal. Animals colonized and shedding E. coli O157:H7 at high levels are a small fraction of animals in a pen but are important source for transferring the pathogen amongst the penmates. Recent research has indicated that diet may greatly influence the shedding of E. coli O157:H7. In addition, diet can influence the microbiota composition of the feces. However, little is known about the interaction between the indigenous microbiota and fecal shedding of E. coli O157:H7. Understanding the influence of indigenous microbiota on the colonization and shedding of E. coli O157:H7 will provide a potential avenue for intervention in the preharvest production environment not yet exploited.

  8. Efeito do tempo de conservação de polimorfonucleares do sangue de bezerros sobre o metabolismo oxidativo e a atividade de fagocitose de Escherichia coli

    OpenAIRE

    BOHLAND, Elizabeth; SÁ-ROCHA, Vanessa de Moura; CYRILLO, Fernanda Cavallini; BENESI, Fernando José

    2008-01-01

    Foram avaliados os efeitos do tempo sobre o metabolismo oxidativo e a fagocitose de Escherichia coli, em amostras de polimorfonucleares (PMN) do sangue, de cinco bezerros hígidos, conservadas em banho de gelo por duas (t2), quatro (t4), seis (t6), 12 (t12) e 24 (t24) horas. O metabolismo oxidativo foi avaliado utilizando o Diacetato 2' 7' Diclorofluoresceína (DCFH-DA) e a E. coli, como estímulo. Para a fagocitose a mesma bactéria foi utilizada. As amostras foram analisadas por citometria de f...

  9. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors

    DEFF Research Database (Denmark)

    Benítez-Páez, Alfonso; Villarroya, Magda; Douthwaite, Stephen Roger

    2010-01-01

    to uncover candidate E. coli genes for the missing enzyme(s). Transfer RNAs from null mutants for candidate genes were analyzed by mass spectrometry and revealed that inactivation of yibK leads to loss of 2'-O-methylation at position 34 in both tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Loss of Yib...... of the wobble nucleotide; YibK recognition of this target requires a pyridine at position 34 and N⁶-(isopentenyl)-2-methylthioadenosine at position 37. YibK is one of the last remaining E. coli tRNA modification enzymes to be identified and is now renamed TrmL.......Transfer RNAs are the most densely modified nucleic acid molecules in living cells. In Escherichia coli, more than 30 nucleoside modifications have been characterized, ranging from methylations and pseudouridylations to more complex additions that require multiple enzymatic steps. Most...

  10. Hard copies for digital medical images: an overview

    Science.gov (United States)

    Blume, Hartwig R.; Muka, Edward

    1995-04-01

    This paper is a condensed version of an invited overview on the technology of film hard-copies used in radiology. Because the overview was given to an essentially nonmedical audience, the reliance on film hard-copies in radiology is outlined in greater detail. The overview is concerned with laser image recorders generating monochrome prints on silver-halide films. The basic components of laser image recorders are sketched. The paper concentrates on the physical parameters - characteristic function, dynamic range, digitization resolution, modulation transfer function, and noise power spectrum - which define image quality and information transfer capability of the printed image. A preliminary approach is presented to compare the printed image quality with noise in the acquired image as well as with the noise of state-of- the-art cathode-ray-tube display systems. High-performance laser-image- recorder/silver-halide-film/light-box systems are well capable of reproducing acquired radiologic information. Most recently development was begun toward a display function standard for soft-copy display systems to facilitate similarity of image presentation between different soft-copy displays as well as between soft- and hard-copy displays. The standard display function is based on perceptional linearization. The standard is briefly reviewed to encourage the printer industry to adopt it, too.

  11. Mitochondrial DNA Copy Number in Sleep Duration Discordant Monozygotic Twins.

    Science.gov (United States)

    Wrede, Joanna E; Mengel-From, Jonas; Buchwald, Dedra; Vitiello, Michael V; Bamshad, Michael; Noonan, Carolyn; Christiansen, Lene; Christensen, Kaare; Watson, Nathaniel F

    2015-10-01

    Mitochondrial DNA (mtDNA) copy number is an important component of mitochondrial function and varies with age, disease, and environmental factors. We aimed to determine whether mtDNA copy number varies with habitual differences in sleep duration within pairs of monozygotic twins. Academic clinical research center. 15 sleep duration discordant monozygotic twin pairs (30 twins, 80% female; mean age 42.1 years [SD 15.0]). Sleep duration was phenotyped with wrist actigraphy. Each twin pair included a "normal" (7-9 h/24) and "short" (sleeping twin. Fasting peripheral blood leukocyte DNA was assessed for mtDNA copy number via the n-fold difference between qPCR measured mtDNA and nuclear DNA creating an mtDNA measure without absolute units. We used generalized estimating equation linear regression models accounting for the correlated data structure to assess within-pair effects of sleep duration on mtDNA copy number. Mean within-pair sleep duration difference per 24 hours was 94.3 minutes (SD 62.6 min). We found reduced sleep duration (β = 0.06; 95% CI 0.004, 0.12; P sleep efficiency (β = 0.51; 95% CI 0.06, 0.95; P sleep duration was associated with a decrease in mtDNA copy number of 0.06. Likewise, a 1% decrease in actigraphy-defined sleep efficiency was associated with a decrease in mtDNA copy number of 0.51. Reduced sleep duration and sleep efficiency were associated with reduced mitochondrial DNA copy number in sleep duration discordant monozygotic twins offering a potential mechanism whereby short sleep impairs health and longevity through mitochondrial stress. © 2015 Associated Professional Sleep Societies, LLC.

  12. High density growth of T7 expression strains with auto-induction option

    Energy Technology Data Exchange (ETDEWEB)

    Studier, F. William (Stony Brook, NY)

    2010-07-20

    A bacterial growth medium for promoting auto-induction of transcription of cloned DNA in cultures of bacterial cells grown batchwise is disclosed. The transcription is under the control of a lac repressor. Also disclosed is a bacterial growth medium for improving the production of a selenomethionine-containing protein or polypeptide in a bacterial cell, the protein or polypeptide being produced by recombinant DNA techniques from a lac or T7lac promoter, the bacterial cell encoding a vitamin B12-dependent homocysteine methylase. Finally, disclosed is a bacterial growth medium for suppressing auto-induction of expression in cultures of bacterial cells grown batchwise, said transcription being under the control of lac repressor.

  13. Antimicrobial activities of red wine-based formulations containing plant extracts against Escherichia coli O157:H7 and Salmonella enterica serovar Hadar

    Science.gov (United States)

    We evaluated the bactericidal activities of red wine and red wine solutions containing a commercial olive extract called Hydrox-12, oregano oil, or a mixture of both in red wine against the following foodborne pathogens: Escherichia coli O157:H7, Salmonella enterica, Listeria monocytogenes, and Stap...

  14. Crystallization and preliminary crystallographic analysis of an Escherichia coli-selected mutant of the nuclease domain of the metallonuclease colicin E7

    DEFF Research Database (Denmark)

    Czene, Aniko; Toth, Eszter; Gyurcsik, Bela

    2013-01-01

    The metallonuclease colicin E7 is a member of the HNH family of endonucleases. It serves as a bacterial toxin in Escherichia coli, protecting the host cell from other related bacteria and bacteriophages by degradation of their chromosomal DNA under environmental stress. Its cell-killing activity ....... X-ray diffraction data were collected to 1.6 Å resolution and could be indexed and averaged in the trigonal space group P3121 or P3221, with unit-cell parameters a = b = 55.4, c = 73.1 Å. Structure determination by molecular replacement is in progress.......The metallonuclease colicin E7 is a member of the HNH family of endonucleases. It serves as a bacterial toxin in Escherichia coli, protecting the host cell from other related bacteria and bacteriophages by degradation of their chromosomal DNA under environmental stress. Its cell-killing activity...... is attributed to the nonspecific nuclease domain (NColE7), which possesses the catalytic ββα-type metal ion-binding HNH motif at its C-terminus. Mutations affecting the positively charged amino acids at the N-terminus of NColE7 (444-576) surprisingly showed no or significantly reduced endonuclease activity...

  15. High-Resolution 7T MR Imaging of the Motor Cortex in Amyotrophic Lateral Sclerosis.

    Science.gov (United States)

    Cosottini, M; Donatelli, G; Costagli, M; Caldarazzo Ienco, E; Frosini, D; Pesaresi, I; Biagi, L; Siciliano, G; Tosetti, M

    2016-03-01

    Amyotrophic lateral sclerosis is a progressive motor neuron disorder that involves degeneration of both upper and lower motor neurons. In patients with amyotrophic lateral sclerosis, pathologic studies and ex vivo high-resolution MR imaging at ultra-high field strength revealed the co-localization of iron and activated microglia distributed in the deep layers of the primary motor cortex. The aims of the study were to measure the cortical thickness and evaluate the distribution of iron-related signal changes in the primary motor cortex of patients with amyotrophic lateral sclerosis as possible in vivo biomarkers of upper motor neuron impairment. Twenty-two patients with definite amyotrophic lateral sclerosis and 14 healthy subjects underwent a high-resolution 2D multiecho gradient-recalled sequence targeted on the primary motor cortex by using a 7T scanner. Image analysis consisted of the visual evaluation and quantitative measurement of signal intensity and cortical thickness of the primary motor cortex in patients and controls. Qualitative and quantitative MR imaging parameters were correlated with electrophysiologic and laboratory data and with clinical scores. Ultra-high field MR imaging revealed atrophy and signal hypointensity in the deep layers of the primary motor cortex of patients with amyotrophic lateral sclerosis with a diagnostic accuracy of 71%. Signal hypointensity of the deep layers of the primary motor cortex correlated with upper motor neuron impairment (r = -0.47; P amyotrophic lateral sclerosis. Cortical thinning and signal hypointensity of the deep layers of the primary motor cortex could constitute a marker of upper motor neuron impairment in patients with amyotrophic lateral sclerosis. © 2016 by American Journal of Neuroradiology.

  16. Detection and Verification of the Viable but Nonculturable (VBNC) State of Escherichia coli O157:H7 and Listeria monocytogenes Using Flow Cytometry and Standard Plating.

    Science.gov (United States)

    Afari, George Kwabena; Hung, Yen-Con

    2018-06-15

    The use of electrolyzed oxidizing (EO) water to inactivate microorganisms on foods has been extensively studied and shown to be effective. However, the prospect of the formation of "viable but nonculturable" (VBNC) cells in pathogens after low free chlorine concentration (FCC) treatments under high organic loads presents safety concerns. This study investigated the effect of EO water FCC on inducing Escherichia coli O157:H7 and Listeria monocytogenes into the VBNC state and studied possible resuscitation triggering procedures of the VBNC cells. A 5-strain cocktail of each pathogen (10 6 colony forming units [CFU]/mL) was exposed to EO water (FCC of 20, 10, 5, 2.5, 1.25, 0.625 mg/L) and allowed to stand for 1 and 5 min, followed by the addition of neutralizing broth. Treated samples were plated on nonselective agar and analyzed using flow cytometry. For resuscitation, samples treated with identified VBNC induction conditions were exposed to elevated temperatures (37 °C) as well as addition of sodium pyruvate (SP) and Tween® 20 (T20) solutions. The initial culturing procedures suggested complete inactivation of both pathogens at 2.5 and 1.25 mg/L FCC in the growth medium. However, flow cytometry profiles showed VBNC cells were present. Subjecting samples to the recovery procedures further proved that VBNC E. coli O157:H7 can be resuscitated after exposure to SP and T20 at 37 °C, while L. monocytogenes did not resuscitate. These findings show that treating pathogens at low FCC can induce the VBNC state, and culturability of E. coli O157:H7 can be restored under appropriate conditions. VBNC induction conditions for foodborne pathogens during chlorine washing treatment were determined in a broth system and the information can serve as a basis for future studies that address the prevention of VBNC formation during produce wash treatments. © 2018 Institute of Food Technologists®.

  17. Effectiveness of different antimicrobial washes combined with freezing against Escherichia coli O157:H7, Salmonella Typhimurium, and Listeria monocytogenes inoculated on blueberries

    Science.gov (United States)

    To ensure the microbial safety of produce including blueberries, sanitization is a critical step. This study evaluated the efficacy of sanitizers when coupled with frozen storage, in inactivating Escherichia coli O157:H7, Salmonella Typhimurium and Listeria monocytogenes inoculated on wild blueberri...

  18. Myxoma virus M-T7, a secreted homolog of the interferon-gamma receptor, is a critical virulence factor for the development of myxomatosis in European rabbits.

    Science.gov (United States)

    Mossman, K; Nation, P; Macen, J; Garbutt, M; Lucas, A; McFadden, G

    1996-01-01

    Myxoma virus is a leporipoxvirus of New World rabbits (Sylvilagus sp.) that induces a rapidly lethal infection known as myxomatosis in the European rabbit (Oryctolagus cuniculus). Like all poxviruses, myxoma virus encodes a plethora of proteins to circumvent or inhibit a variety of host antiviral immune mechanisms. M-T7, the most abundantly secreted protein of myxoma virus-infected cells, was originally identified as an interferon-gamma receptor homolog (Upton, Mossman, and McFadden, Science 258, 1369-1372, 1992). Here, we demonstrate that M-T7 is dispensable for virus replication in cultured cells but is a critical virulence factor for virus pathogenesis in European rabbits. Disruption of both copies of the M-T7 gene in myxoma virus was achieved by the deletion of 372 bp of M-T7 coding sequences, replacement with a selectable marker, p7.5Ecogpt, and selection of a recombinant virus (vMyxlac-T7gpt) resistant to mycophenolic acid. vMyxlac-T7gpt expressed no detectable M-T7 protein and infected cells supernatants were devoid of any detectable interferon-gamma binding activities. Immunohistochemical staining with anti-beta-galactosidase and anti-CD43 antibodies demonstrated that in vMyxlac-T7gpt-infected rabbits the loss of M-T7 not only caused a dramatic reduction in disease symptoms and viral dissemination to secondary sites, but also dramatically influenced host leukocyte behavior. Notably, primary lesions in wild-type virus infections were generally underlayed by large masses of inflammatory cells that did not effectively migrate into the dermal sites of viral replication, whereas in vMyxlac-T7gpt infections this apparent block to leukocyte influx was relieved. A second major phenotypic distinction noted for the M-T7 knockout virus was the extensive activation of lymphocytes in secondary immune organs, particularly the spleen and lymph nodes, by Day 4 of the infection. This is in stark contrast to infection by wild-type myxoma virus, which results in relatively

  19. Junction structures based on the high-Tc superconductor YBa2Cu3O7

    International Nuclear Information System (INIS)

    Gijs, M.A.M.

    1993-01-01

    An overview is given of the investigations of the Josephson effect in junction structures based on the high-T c superconductor YBa 2 Cu 3 O 7-δ , which were carried out at the Philips Research Laboratories in Eindhoven in the 1988-1990 period. The reported results are presented in their international scientific context, without attempting a complete review of the subject. However, the various junction types studied give a good idea of the scientific pursuits of high-T c junction researchers in this period. The following junctions are considered: in the category of 'weak link'-type junctions we have investigated YBa 2 Cu 3 O 7-δ -Ag-Nb point contact junctions, YBa 2 Cu 3 O 7-δ Dayem bridges and YBa 2 Cu 3 O 7-δ -Ag(-Al)-Pb proximity junctions. In these structures we combine a high-T c with a low-T c superconductor. We also fabricated planar 'all high-T c ' YBa 2 Cu 3 O 7-δ -Ag-YBa 2 Cu 3 O 7-δ junctions using a submicron structuring process. Next we have made tunnel junctions to study density of states effects of the high-T c superconductor : YBa 2 Cu 3 O 7-δ -Pb junctions using the degraded YBa 2 Cu 3 O 7-δ -Pb interface as a tunnel barrier, and YBa 2 Cu 3 O 7-δ -Ag-Al/Al 2 O 3 /Pb tunnel junctions based on the superconducting proximity effect. Our junction structures are electrically characterized and mostly studied in microwave and magnetic fields. Results are compared with current theoretical models. (orig.)

  20. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

    Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

  1. Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach.

    Directory of Open Access Journals (Sweden)

    Christiaan Klijn

    2010-01-01

    Full Text Available Tumorigenesis is a multi-step process in which normal cells transform into malignant tumors following the accumulation of genetic mutations that enable them to evade the growth control checkpoints that would normally suppress their growth or result in apoptosis. It is therefore important to identify those combinations of mutations that collaborate in cancer development and progression. DNA copy number alterations (CNAs are one of the ways in which cancer genes are deregulated in tumor cells. We hypothesized that synergistic interactions between cancer genes might be identified by looking for regions of co-occurring gain and/or loss. To this end we developed a scoring framework to separate truly co-occurring aberrations from passenger mutations and dominant single signals present in the data. The resulting regions of high co-occurrence can be investigated for between-region functional interactions. Analysis of high-resolution DNA copy number data from a panel of 95 hematological tumor cell lines correctly identified co-occurring recombinations at the T-cell receptor and immunoglobulin loci in T- and B-cell malignancies, respectively, showing that we can recover truly co-occurring genomic alterations. In addition, our analysis revealed networks of co-occurring genomic losses and gains that are enriched for cancer genes. These networks are also highly enriched for functional relationships between genes. We further examine sub-networks of these networks, core networks, which contain many known cancer genes. The core network for co-occurring DNA losses we find seems to be independent of the canonical cancer genes within the network. Our findings suggest that large-scale, low-intensity copy number alterations may be an important feature of cancer development or maintenance by affecting gene dosage of a large interconnected network of functionally related genes.

  2. Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat.

    Science.gov (United States)

    Zhu, Jie; Pearce, Stephen; Burke, Adrienne; See, Deven Robert; Skinner, Daniel Z; Dubcovsky, Jorge; Garland-Campbell, Kimberly

    2014-05-01

    The interaction between VRN - A1 and FR - A2 largely affect the frost tolerance of hexaploid wheat. Frost tolerance is critical for wheat survival during cold winters. Natural variation for this trait is mainly associated with allelic differences at the VERNALIZATION 1 (VRN1) and FROST RESISTANCE 2 (FR2) loci. VRN1 regulates the transition between vegetative and reproductive stages and FR2, a locus including several tandemly duplicated C-REPEAT BINDING FACTOR (CBF) transcription factors, regulates the expression of Cold-regulated genes. We identified sequence and copy number variation at these two loci among winter and spring wheat varieties and characterized their association with frost tolerance. We identified two FR-A2 haplotypes-'FR-A2-S' and 'FR-A2-T'-distinguished by two insertion/deletions and ten single nucleotide polymorphisms within the CBF-A12 and CBF-A15 genes. Increased copy number of CBF-A14 was frequently associated with the FR-A2-T haplotype and with higher CBF14 transcript levels in response to cold. Factorial ANOVAs revealed significant interactions between VRN1 and FR-A2 for frost tolerance in both winter and spring panels suggesting a crosstalk between vernalization and cold acclimation pathways. The model including these two loci and their interaction explained 32.0 and 20.7 % of the variation in frost tolerance in the winter and spring panels, respectively. The interaction was validated in a winter wheat F 4:5 population segregating for both genes. Increased VRN-A1 copy number was associated with improved frost tolerance among varieties carrying the FR-A2-T allele but not among those carrying the FR-A2-S allele. These results suggest that selection of varieties carrying the FR-A2-T allele and three copies of the recessive vrn-A1 allele would be a good strategy to improve frost tolerance in wheat.

  3. Local copying of orthogonal entangled quantum states

    International Nuclear Information System (INIS)

    Anselmi, Fabio; Chefles, Anthony; Plenio, Martin B

    2004-01-01

    In classical information theory one can, in principle, produce a perfect copy of any input state. In quantum information theory, the no cloning theorem prohibits exact copying of non-orthogonal states. Moreover, if we wish to copy multiparticle entangled states and can perform only local operations and classical communication (LOCC), then further restrictions apply. We investigate the problem of copying orthogonal, entangled quantum states with an entangled blank state under the restriction to LOCC. Throughout, the subsystems have finite dimension D. We show that if all of the states to be copied are non-maximally entangled, then novel LOCC copying procedures based on entanglement catalysis are possible. We then study in detail the LOCC copying problem where both the blank state and at least one of the states to be copied are maximally entangled. For this to be possible, we find that all the states to be copied must be maximally entangled. We obtain a necessary and sufficient condition for LOCC copying under these conditions. For two orthogonal, maximally entangled states, we provide the general solution to this condition. We use it to show that for D = 2, 3, any pair of orthogonal, maximally entangled states can be locally copied using a maximally entangled blank state. However, we also show that for any D which is not prime, one can construct pairs of such states for which this is impossible

  4. High-field paramagnetic Meissner effect up to 14 T in melt-textured YBa_2Cu_3O_7_–_δ

    International Nuclear Information System (INIS)

    Dias, F.T.; Vieira, V.N.; Wolff-Fabris, F.; Kampert, E.; Gouvêa, C.P.; Campos, A.P.C.; Archanjo, B.S.; Schaf, J.; Obradors, X.; Puig, T.; Roa, J.J.; Sahoo, B.K.

    2016-01-01

    Highlights: • A persistent paramagnetic Meissner effect up to 14 T. • The PME with a slight tendency to saturate in high magnetic fields. • Strong time effects causing a paramagnetic relaxation dependent on the cooling rate. - Abstract: We have performed magnetization experiments in a melt-textured YBa_2Cu_3O_7_-_δ (Y123) sample with Y_2BaCuO_5 (Y211) inclusions, under magnetic fields up to 14 T applied parallel or perpendicular to the ab plane. Magnetic anisotropy and paramagnetic moments were observed in both FC (field-cooling) and FCW (field-cooled warming) procedures and these features correspond to the so-called High-Field Paramagnetic Meissner Effect (HFPME). The HFPME effect increases monotonically as the magnetic field rises and a strong paramagnetic relaxation, toward increasing paramagnetic moment was additionally observed as a function of time. Microscopy analysis revealed a complex and correlated microstructure of the Y211 particles. These correlated defects are well known to cause strong flux pinning. Our results suggest a scenario of strong flux compression within weak or non-superconducting regions of the samples, developed as a consequence of the Meissner effect and assisted by strong flux pinning by the Y211 particles. This scenario is observed up to 14 T and clearly persists beyond.

  5. Heat resistance of Escherichia coli O157:H7 in apple juice.

    Science.gov (United States)

    Splittstoesser, D F; McLellan, M R; Churey, J J

    1996-03-01

    The objective was to determine the effect of cider composition on the heat resistance of Escherichia coli O157:H7. The average D52 value in a model Empire apple juice was 18 min with a z value of 4.8 degrees C. Increasing the Brix from 11.8 to 16.5 degrees had no effect on thermal resistance, while increasing L-malic acid from 0.2 to 0.8%, or reducing the pH from 4.4 to 3.6 sensitized the cells to heat. The greatest effect on heat resistance was afforded by the preservatives benzoic and sorbic acids: D50 values in ciders containing 1,000 mg/l were 5.2 min in the presence of sorbic acid and only 0.64 min in the presence of benzoic acid. Commercial apple juice concentrates yielded lower numbers of survivors than single-strength juices even though their higher sugar concentrations of about 46 degrees Brix increased heat resistance.

  6. Optimal design of a 7 T highly homogeneous superconducting magnet for a Penning trap

    International Nuclear Information System (INIS)

    Wu Wei; He Yuan; Ma Lizhen; Huang Wenxue; Xia Jiawen

    2010-01-01

    A Penning trap system called Lanzhou Penning Trap (LPT) is now being developed for precise mass measurements at the Institute of Modern Physics(IMP). One of the key components is a 7 T actively shielded superconducting magnet with a clear warm bore of 156 mm. The required field homogeneity is 3 x 10 -7 over two 1 cubic centimeter volumes lying 220 mm apart along the magnet axis. We introduce a two-step method which combines linear programming and a nonlinear optimization algorithm for designing the multi-section superconducting magnet. This method is fast and flexible for handling arbitrary shaped homogeneous volumes and coils. With the help of this method an optimal design for the LPT superconducting magnet has been obtained. (authors)

  7. Uterine Artery Embolization for Symptomatic Fibroids with High Signal Intensity on T2-Weighted MR Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Suyon; Kim, Man Deuk; Lee, Myung Su; Lee, Mu Sook; Park, Sung Il; Won, Jong Yun; Lee, Do Yun; Lee, Kwang Hun [Dept. of Radiology, Research Institute of Radiological Science, Yonsei University College of Medicine, Severance Hospital, Seoul (Korea, Republic of)

    2012-09-15

    To evaluate the effectiveness of uterine artery embolization (UAE) for treating symptomatic fibroids with high signal intensity (SI) on magnetic resonance (MR) T2-weighted imaging (T2WI). A total of 537 cases, consisting of 14 patients with high SI fibroids on T2WI (T2 high group), were retrospectively included and compared with 28 randomly selected patients with low SI fibroids on T2WI (control group). High SI of a predominant fibroid on T2WI was defined as having the same or higher SI than the myometrium. Patient ages ranged from 28 to 52 years (mean, 38.1 years). All patients underwent MRI before and after UAE. Predominant fibroid and uterine volumes were calculated with MR images. Symptom status in terms of menorrhagia and dysmenorrhea was scored on a scale of 0-10, with 0 being no symptoms and 10 being the baseline, or initial symptoms. Of the patients in the T2 high group, 13 out of 14 (92.9%) patients demonstrated complete necrosis of the predominant fibroids. The mean volume reduction rates of the predominant fibroids in the T2 high group was 61.7% at three months after UAE, which was significantly higher than the volume reduction rates of 42.1% noted in the control group (p < 0.05). Changes in symptom scores for menorrhagia and dysmenorrhea after UAE (baseline score minus follow-up score) were 4.9 and 7.5 in T2 high group and they were 5.0 and 7.7 in control group, suggesting a significant resolution of symptoms (p < 0.01) in both groups but no significant difference between the two groups. UAE is effective for uttering fibroids showing high SI on T2WI. The mean volume reduction rate of the predominant fibroids three months after UAE was greater in the T2 high group than in the control group.

  8. Uterine Artery Embolization for Symptomatic Fibroids with High Signal Intensity on T2-Weighted MR Imaging

    International Nuclear Information System (INIS)

    Chang, Suyon; Kim, Man Deuk; Lee, Myung Su; Lee, Mu Sook; Park, Sung Il; Won, Jong Yun; Lee, Do Yun; Lee, Kwang Hun

    2012-01-01

    To evaluate the effectiveness of uterine artery embolization (UAE) for treating symptomatic fibroids with high signal intensity (SI) on magnetic resonance (MR) T2-weighted imaging (T2WI). A total of 537 cases, consisting of 14 patients with high SI fibroids on T2WI (T2 high group), were retrospectively included and compared with 28 randomly selected patients with low SI fibroids on T2WI (control group). High SI of a predominant fibroid on T2WI was defined as having the same or higher SI than the myometrium. Patient ages ranged from 28 to 52 years (mean, 38.1 years). All patients underwent MRI before and after UAE. Predominant fibroid and uterine volumes were calculated with MR images. Symptom status in terms of menorrhagia and dysmenorrhea was scored on a scale of 0-10, with 0 being no symptoms and 10 being the baseline, or initial symptoms. Of the patients in the T2 high group, 13 out of 14 (92.9%) patients demonstrated complete necrosis of the predominant fibroids. The mean volume reduction rates of the predominant fibroids in the T2 high group was 61.7% at three months after UAE, which was significantly higher than the volume reduction rates of 42.1% noted in the control group (p < 0.05). Changes in symptom scores for menorrhagia and dysmenorrhea after UAE (baseline score minus follow-up score) were 4.9 and 7.5 in T2 high group and they were 5.0 and 7.7 in control group, suggesting a significant resolution of symptoms (p < 0.01) in both groups but no significant difference between the two groups. UAE is effective for uttering fibroids showing high SI on T2WI. The mean volume reduction rate of the predominant fibroids three months after UAE was greater in the T2 high group than in the control group.

  9. Time-resolved phosphorous magnetization transfer of the human calf muscle at 3 T and 7 T: A feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    Valkovič, Ladislav, E-mail: siegfried.trattnig@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Institute of Measurement Science, Department of Imaging Methods, Slovak Academy of Sciences, 841 04 Bratislava, Dúbravska cesta 9 (Slovakia); Chmelík, Marek, E-mail: marek.chmelik@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Just Kukurova, Ivica, E-mail: ivica.kukurova@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Krššák, Martin, E-mail: martin.krssak@meduniwien.ac.at [Department of Internal Medicine III, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Gruber, Stephan, E-mail: stephan@nmr.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Frollo, Ivan, E-mail: umerollo@savba.sk [Institute of Measurement Science, Department of Imaging Methods, Slovak Academy of Sciences, 841 04 Bratislava, Dúbravska cesta 9 (Slovakia); Trattnig, Siegfried, E-mail: siegfried.trattnig@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Bogner, Wolfgang, E-mail: wolfgang@nmr.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria)

    2013-05-15

    Phosphorous ({sup 31}P) magnetization transfer (MT) experiments enable the non-invasive investigation of human muscle metabolism in various physiological and pathological conditions. The purpose of our study was to investigate the feasibility of time-resolved MT, and to compare the results of MT experiments at 3 T and 7 T. Six healthy volunteers were examined on a 3 T and a 7 T MR scanner using the same setup and identical measurement protocols. In the calf muscle of all volunteers, four separate MT experiments (each ∼10 min duration) were performed in one session. The forward rate constant of the ATP synthesis reaction (k{sub ATP}) and creatine kinase reaction (k{sub CK}), as well as corresponding metabolic fluxes (F{sub ATP}, F{sub CK}), were estimated. A comparison of these exchange parameters, apparent T{sub 1}s, data quality, quantification precision, and reproducibility was performed. The data quality and reproducibility of the same MT experiments at 7 T was significantly higher (i.e., k{sub ATP} 2.7 times higher and k{sub CK} 3.4 times higher) than at 3 T (p < 0.05). The values for k{sub ATP} (p = 0.35) and k{sub CK} (p = 0.09) at both field strengths were indistinguishable. Even a single MT experiment at 7 T provided better data quality than did a 4 times-longer MT experiment at 3 T. The minimal time-resolution to reliably quantify both F{sub ATP} and F{sub CK} at 7 T was ∼6 min. Our results show that MT experiments at 7 T can be at least 4 times faster than 3 T MT experiments and still provide significantly better quantification. This enables time-resolved MT experiments for the observation of slow metabolic changes in the human calf muscle at 7 T.

  10. Time-resolved phosphorous magnetization transfer of the human calf muscle at 3 T and 7 T: A feasibility study

    International Nuclear Information System (INIS)

    Valkovič, Ladislav; Chmelík, Marek; Just Kukurova, Ivica; Krššák, Martin; Gruber, Stephan; Frollo, Ivan; Trattnig, Siegfried; Bogner, Wolfgang

    2013-01-01

    Phosphorous ( 31 P) magnetization transfer (MT) experiments enable the non-invasive investigation of human muscle metabolism in various physiological and pathological conditions. The purpose of our study was to investigate the feasibility of time-resolved MT, and to compare the results of MT experiments at 3 T and 7 T. Six healthy volunteers were examined on a 3 T and a 7 T MR scanner using the same setup and identical measurement protocols. In the calf muscle of all volunteers, four separate MT experiments (each ∼10 min duration) were performed in one session. The forward rate constant of the ATP synthesis reaction (k ATP ) and creatine kinase reaction (k CK ), as well as corresponding metabolic fluxes (F ATP , F CK ), were estimated. A comparison of these exchange parameters, apparent T 1 s, data quality, quantification precision, and reproducibility was performed. The data quality and reproducibility of the same MT experiments at 7 T was significantly higher (i.e., k ATP 2.7 times higher and k CK 3.4 times higher) than at 3 T (p < 0.05). The values for k ATP (p = 0.35) and k CK (p = 0.09) at both field strengths were indistinguishable. Even a single MT experiment at 7 T provided better data quality than did a 4 times-longer MT experiment at 3 T. The minimal time-resolution to reliably quantify both F ATP and F CK at 7 T was ∼6 min. Our results show that MT experiments at 7 T can be at least 4 times faster than 3 T MT experiments and still provide significantly better quantification. This enables time-resolved MT experiments for the observation of slow metabolic changes in the human calf muscle at 7 T

  11. Detection and characterization of Escherichia coli O157:H7 from feral pigeon in Qom province, Iran

    Directory of Open Access Journals (Sweden)

    Hossein Esameili

    2015-02-01

    Full Text Available Objective: To detect and characterize Escherichia coli (E. coli O157:H7 in feral pigeons in Qom province, Iran. Methods: In this survey, 290 cloacal samples were obtained from trapped feral pigeons in Qom province. Microbiological, biochemical and serological examinations were done to detect the E. coli O157:H7. Isolates were subjected to multiplex polymerase chain reaction for the detection of stx1, stx2, eaeA and hlyA genes. Results: Four samples (1.38% were positive for E. coli O157:H7 by using O157 and H7 antisera and only one E. coli O157:H7 strain isolated showed the presence of stx1, stx2, eaeA and hlyA genes. Conclusions: The results of present survey revealed that feral pigeons in Qom province had the potential to be a reservoir of E. coli O157:H7. The low prevalence of E. coli O157:H7 can be attributed to sampling each pigeon just once and fecal culture limits, and true prevalence of the E. coli O157:H7 might be higher than our findings.

  12. Profound protection against respiratory challenge with a lethal H7N7 influenza A virus by increasing the magnitude of CD8(+) T-cell memory

    DEFF Research Database (Denmark)

    Christensen, Jan Pravsgaard; Doherty, P C; Branum, K C

    2000-01-01

    The recall of CD8(+) T-cell memory established by infecting H-2(b) mice with an H1N1 influenza A virus provided a measure of protection against an extremely virulent H7N7 virus. The numbers of CD8(+) effector and memory T cells specific for the shared, immunodominant D(b)NP(366) epitope were...... greatly increased subsequent to the H7N7 challenge, and though lung titers remained as high as those in naive controls for 5 days or more, the virus was cleared more rapidly. Expanding the CD8(+) memory T-cell pool (10%) by sequential priming with two different influenza A viruses (H3N2-->H1N1......) gave much better protection. Though the H7N7 virus initially grew to equivalent titers in the lungs of naive and double-primed mice, the replicative phase was substantially controlled within 3 days. This tertiary H7N7 challenge caused little increase in the magnitude of the CD8(+) D(b)NP(366)(+) T...

  13. Survival of genetically marked .i.Escherichia coli./i. O157:H7 in soil as affected by soil microbial community shifts

    Czech Academy of Sciences Publication Activity Database

    van Elsas, J.D.; Hill, P.; Chroňáková, Alica; Grekova, M.; Topalova, Y.; Elhottová, Dana; Krištůfek, Václav

    -, č. 1 (2007), s. 204-214 ISSN 1751-7362 R&D Projects: GA MŠk LC06066 Grant - others:NATO(NL) ESP.EAP.CLG 981785 Institutional research plan: CEZ:AV0Z60660521 Source of funding: V - iné verejné zdroje Keywords : soil * fumigation * Escherichia coli O157:H7 Subject RIV: EH - Ecology, Behaviour

  14. Behavior of pulsed electric field injured Escherichia coli O157:H7 cells in apple juice amended with pyruvate and catalase

    Science.gov (United States)

    Pulse Electric Field (PEF) treatment has been used to inactivate bacteria in liquid foods. However, information on the behavior of PEF injured Escherichia coli bacteria in media during storage at 5 and 23C are limited. In this study, we investigated the fate of E. coli O157:H7 cells at 6.8 log CFU/m...

  15. Patterns, correlates, and reduction of homework copying

    Directory of Open Access Journals (Sweden)

    David J. Palazzo

    2010-03-01

    Full Text Available Submissions to an online homework tutor were analyzed to determine whether they were copied. The fraction of copied submissions increased rapidly over the semester, as each weekly deadline approached and for problems later in each assignment. The majority of students, who copied less than 10% of their problems, worked steadily over the three days prior to the deadline, whereas repetitive copiers (those who copied >30% of their submitted problems exerted little effort early. Importantly, copying homework problems that require an analytic answer correlates with a 2(σ decline over the semester in relative score for similar problems on exams but does not significantly correlate with the amount of conceptual learning as measured by pretesting and post-testing. An anonymous survey containing questions used in many previous studies of self-reported academic dishonesty showed ∼1/3 less copying than actually was detected. The observed patterns of copying, free response questions on the survey, and interview data suggest that time pressure on students who do not start their homework in a timely fashion is the proximate cause of copying. Several measures of initial ability in math or physics correlated with copying weakly or not at all. Changes in course format and instructional practices that previous self-reported academic dishonesty surveys and/or the observed copying patterns suggested would reduce copying have been accompanied by more than a factor of 4 reduction of copying from ∼11% of all electronic problems to less than 3%. As expected (since repetitive copiers have approximately three times the chance of failing, this was accompanied by a reduction in the overall course failure rate. Survey results indicate that students copy almost twice as much written homework as online homework and show that students nationally admit to more academic dishonesty than MIT students.

  16. Thermal inactivation of Escherichia coli 0157:H7 (ECOH) and non-0157 Shiga toxin-producing E.coli (STEC)in mechanically tenderized veal

    Science.gov (United States)

    We quantified thermal destruction of Shiga toxin-producing Escherichia coli O157:H7 (ECOH) and Shiga toxin-producing non-O157 E. coli (STEC) cells within mechanically tenderized veal cutlets following cooking on an electric skillet. For each of five trials, flattened veal cutlets (ca. 71.6 g; ca. 1/...

  17. Fate of Escherichia coli O157: H7 in agricultural soils amended with different organic fertilizers.

    Science.gov (United States)

    Yao, Zhiyuan; Yang, Li; Wang, Haizhen; Wu, Jianjun; Xu, Jianming

    2015-10-15

    Five organic fertilizers (vermicompost, pig manure, chicken manure, peat and oil residue) were applied to agricultural soils to study their effects on the survival of Escherichia coli O157:H7 (E. coli O157:H7). Results showed that E. coli O157:H7 survival changed greatly after organic fertilizers application, with shorter td values (survival time needed to reach the detection limit of 100 CFU g(-1)) (12.57±6.57 days) in soils amended with chicken manure and the longest (25.65±7.12 days) in soils amended with pig manure. Soil pH, EC and free Fe/Al (hydro) oxides were significant explanatory factors for E. coli O157:H7 survival in the original soils. Soil constituents (minerals and organic matter) and changes in their surface charges with pH increased the effect of soil pH on E. coli O157:H7 survival. However, electrical conductivity played a more important role in regulating E. coli O157:H7 survival in fertilizer-amended soils. This study highlighted the importance of choosing appropriate organic fertilizers in the preharvest environment to reduce food-borne bacterial contamination. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Genome Architecture and Its Roles in Human Copy Number Variation

    Directory of Open Access Journals (Sweden)

    Lu Chen

    2014-12-01

    Full Text Available Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs, are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.

  19. Dose-dependent effects of Lactobacillus rhamnosus on serum interleukin-17 production and intestinal T-cell responses in pigs challenged with Escherichia coli.

    Science.gov (United States)

    Zhu, Yao-Hong; Li, Xiao-Qiong; Zhang, Wei; Zhou, Dong; Liu, Hao-Yu; Wang, Jiu-Feng

    2014-03-01

    The mechanism underlying the dose effect of probiotics on ameliorating diarrhea has not been fully elucidated. Here, low (1 × 10(9) CFU/ml) or high (1 × 10(11) CFU/ml) doses of Lactobacillus rhamnosus ATCC 7469 were administered orally to piglets for 1 week before F4 (K88)-positive enterotoxigenic Escherichia coli (F4(+) ETEC) challenge. Administration of a low, but not a high, dose of L. rhamnosus decreased the percentage of CD3(+) CD4(+) CD8(-) T cells in the peripheral blood. Notably, transiently increased serum concentrations of interleukin-17A (IL-17A) were observed after F4(+) ETEC challenge in pigs pretreated with a high dose of L. rhamnosus. Administration of L. rhamnosus increased the percentage of the small intestinal lamina propria CD3(+) CD4(+) CD8(-) cells and Peyer's patch CD3(+) CD4(-) CD8(-) and CD3(-) CD4(-) CD8(+) cells. The percentage of ileal intraepithelial CD3(+) CD4(-) CD8(+) cells increased only in the high-dose piglets. Administration of L. rhamnosus downregulated expression of ileal IL-17A after F4(+) ETEC challenge but had no effect on expression of gamma interferon (IFN-γ), IL-12, IL-4, and FOXP3 mRNA in the small intestine. Expression of jejunal IL-2, ileal transforming growth factor β1 (TGF-β1), and ileal IL-10 was upregulated in the low-dose piglets after F4(+) ETEC challenge. Our findings suggest that amelioration of infectious diarrhea in piglets by L. rhamnosus is associated with the generation of lamina propria CD3(+) CD4(+) CD8(-) T cells, the expansion of Peyer's patch CD3(+) CD4(-) CD8(-) and CD3(-) CD4(-) CD8(+) cells, and the attenuation of F4(+) ETEC-induced increase in CD3(+) CD4(+) CD8(+) T cells in the small intestine. However, consumption of high doses of L. rhamnosus may increase levels of serum IL-17A after F4(+) ETEC challenge, thus eliciting a strong proinflammatory response.

  20. Efficacy of integrated treatment of UV light and low dose gamma irradiation on Escherichia coli O157:H7 and Salmonella enterica on grape tomatoes

    Science.gov (United States)

    Efficacy of integrated treatment of UVC and low dose Gamma irradiation to inactivate mixed Strains of Escherichia coli O157:H7 and Salmonella enterica inoculated on whole Grape tomatoes was evaluated. A mixed bacterial cocktail composed of a three strain mixture of E. coli O157:H7 (C9490, E02128 an...

  1. What Librarians Still Don't Know about Free Software

    Science.gov (United States)

    Chudnov, Daniel

    2009-01-01

    Free software isn't about cost, and it isn't about hype, it isn't about taking business away from vendors. It's about four kinds of freedom--the freedom to use the software for any purpose, the freedom to study how the software works, the freedom to modify the software to adapt it to one's needs, and the freedom to copy and share copies of the…

  2. Membrane damage and viability loss of thermally treated and high hydrostatic pressurized E. coli 0157:H7 and Salmonella spp. in apple juice

    Science.gov (United States)

    Differences in membrane damage including leakage of intracellular UV-materials and loss of viability of Salmonella spp. and Escherichia coli O157:H7 bacteria in apple juice following thermal death time disk (TDT) and high hydrostatic pressure treatments were investigated. Salmonella and E. coli O157...

  3. Injury and recovery of salmonella, Escherichia coli 0157:H7 and Listeria Monocytogenes on cantaloupe rind surfaces after hyrdogren peroxide and minimal thermal treatment

    Science.gov (United States)

    Introduction: Produce surface structures vary and complicate decontamination treatments for reducing attached bacteria. Purpose: The objective of this study on survival and recovery of injured population of Salmonella, Escherichia coli O157:H7 and Listeria monocytogenes on cantaloupe rind surfaces...

  4. Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA

    NARCIS (Netherlands)

    Etson, Candice M.; Hamdan, Samir M.; Richardson, Charles C.; Oijen, Antoine M. van; Richardson, Charles C.

    2010-01-01

    The DNA polymerases involved in DNA replication achieve high processivity of nucleotide incorporation by forming a complex with processivity factors. A model system for replicative DNA polymerases, the bacteriophage T7 DNA polymerase (gp5), encoded by gene 5, forms a tight, 1:1 complex with

  5. Heterogeneous genetic diversity pattern in Plasmodium vivax genes encoding merozoite surface proteins (MSP) -7E, -7F and -7L.

    Science.gov (United States)

    Garzón-Ospina, Diego; Forero-Rodríguez, Johanna; Patarroyo, Manuel A

    2014-12-13

    The msp-7 gene has become differentially expanded in the Plasmodium genus; Plasmodium vivax has the highest copy number of this gene, several of which encode antigenic proteins in merozoites. DNA sequences from thirty-six Colombian clinical isolates from P. vivax (pv) msp-7E, -7F and -7L genes were analysed for characterizing and studying the genetic diversity of these pvmsp-7 members which are expressed during the intra-erythrocyte stage; natural selection signals producing the variation pattern so observed were evaluated. The pvmsp-7E gene was highly polymorphic compared to pvmsp-7F and pvmsp-7L which were seen to have limited genetic diversity; pvmsp-7E polymorphism was seen to have been maintained by different types of positive selection. Even though these copies seemed to be species-specific duplications, a search in the Plasmodium cynomolgi genome (P. vivax sister taxon) showed that both species shared the whole msp-7 repertoire. This led to exploring the long-term effect of natural selection by comparing the orthologous sequences which led to finding signatures for lineage-specific positive selection. The results confirmed that the P. vivax msp-7 family has a heterogeneous genetic diversity pattern; some members are highly conserved whilst others are highly diverse. The results suggested that the 3'-end of these genes encode MSP-7 proteins' functional region whilst the central region of pvmsp-7E has evolved rapidly. The lineage-specific positive selection signals found suggested that mutations occurring in msp-7s genes during host switch may have succeeded in adapting the ancestral P. vivax parasite population to humans.

  6. Selection of antibiotics in detection procedure of Escherichia coli O157:H7 in vegetables

    Science.gov (United States)

    Hoang, Hoang A.; Nhung, Nguyen T. T.

    2017-09-01

    Detection of Escherichia coli O157:H7 in ready-to-eat fresh vegetables is important since this bacteria is considered as one of the most important pathogens in relation to public health. However, it could be a big challenge for detection of initial low concentrations of E. coli O157:H7 in the samples. In this study, selection of antibiotics that suppress growth of background bacteria to enable detection of E. coli O157:H7 in ready-to-eat fresh vegetables was investigated. Firstly, different combinations of two antibiotics, i.e. novobiocin (N) and vancomycin (V), in BHI broth were conducted. The three antibiotic combinations were preliminary examined their effect on the growth of E. coli O157:H7 and Bacillus spp. in broth based on OD600nm measurement. The combination of both the antibiotics was selected to examine their possibility to support detection of E. coli O157:H7 in vegetables. It was successful when two antibiotics showed their support in detection of E. coli O157:H7 at very low concentration of 2 CFU per one gram of lettuce. Usage of these antibiotics is simple and cheap in the detection procedure and could be applied to other types of ready-to-eat fresh vegetables popular in Vietnam.

  7. Transfer, attachment, and formation of biofilms by Escherichia coli O157:H7 on meat-contact surface materials.

    Science.gov (United States)

    Simpson Beauchamp, Catherine; Dourou, Dimitra; Geornaras, Ifigenia; Yoon, Yohan; Scanga, John A; Belk, Keith E; Smith, Gary C; Nychas, George-John E; Sofos, John N

    2012-06-01

    Studies examined the effects of meat-contact material types, inoculation substrate, presence of air at the liquid-solid surface interface during incubation, and incubation substrate on the attachment/transfer and subsequent biofilm formation by Escherichia coli O157:H7 on beef carcass fabrication surface materials. Materials studied as 2 × 5 cm coupons included stainless steel, acetal, polypropylene, and high-density polyethylene. A 6-strain rifampicin-resistant E. coli O157:H7 composite was used to inoculate (6 log CFU/mL, g, or cm²) tryptic soy broth (TSB), beef fat/lean tissue homogenate (FLH), conveyor belt-runoff fluids, ground beef, or beef fat. Coupons of each material were submerged (4 °C, 30 min) in the inoculated fluids or ground beef, or placed between 2 pieces of inoculated beef fat with pressure (20 kg) applied. Attachment/transfer of the pathogen was surface material and substrate dependent, although beef fat appeared to negate differences among surface materials. Beef fat was the most effective (P transfer and subsequent biofilm formation by E. coli O157:H7. The results highlight the importance of thoroughly cleaning soiled surfaces to remove all remnants of beef fat or other organic material that may harbor or protect microbial contaminants during otherwise lethal antimicrobial interventions. © 2012 Institute of Food Technologists®

  8. Breast MRI at 7 Tesla with a bilateral coil and T1-weighted acquisition with robust fat suppression: image evaluation and comparison with 3 Tesla.

    Science.gov (United States)

    Brown, Ryan; Storey, Pippa; Geppert, Christian; McGorty, KellyAnne; Leite, Ana Paula Klautau; Babb, James; Sodickson, Daniel K; Wiggins, Graham C; Moy, Linda

    2013-11-01

    To evaluate the image quality of T1-weighted fat-suppressed breast MRI at 7 T and to compare 7-T and 3-T images. Seventeen subjects were imaged using a 7-T bilateral transmit-receive coil and 3D gradient echo sequence with adiabatic inversion-based fat suppression (FS). Images were graded on a five-point scale and quantitatively assessed through signal-to-noise ratio (SNR), fibroglandular/fat contrast and signal uniformity measurements. Image scores at 7 and 3 T were similar on standard-resolution images (1.1 × 1.1 × 1.1-1.6 mm(3)), indicating that high-quality breast imaging with clinical parameters can be performed at 7 T. The 7-T SNR advantage was underscored on 0.6-mm isotropic images, where image quality was significantly greater than at 3 T (4.2 versus 3.1, P ≤ 0.0001). Fibroglandular/fat contrast was more than two times higher at 7 T than at 3 T, owing to effective adiabatic inversion-based FS and the inherent 7-T signal advantage. Signal uniformity was comparable at 7 and 3 T (P coil and adiabatic inversion-based FS technique produce image quality that is as good as or better than at 3 T. • High image quality bilateral breast MRI is achievable with clinical parameters at 7 T. • 7-T high-resolution imaging improves delineation of subtle soft tissue structures. • Adiabatic-based fat suppression provides excellent fibroglandular/fat contrast at 7 T. • 7- and 3-T 3D T1-weighted gradient-echo images have similar signal uniformity. • The 7-T dual solenoid coil enables bilateral imaging without compromising uniformity.

  9. The effect of a probiotic Escherichia coli strain on regulatory T-cells in six year-old children.

    Science.gov (United States)

    Hrdý, J; Kocourková, I; Lodinová-Žádníková, R; Kolářová, L; Prokešová, L

    2016-11-30

    Probiotics are believed to prevent or reduce allergy development but the mechanism of their beneficial effect is still poorly understood. Immune characteristics of regulatory T cells (Tregs) in peripheral blood of perinatally probiotic-supplemented children of allergic mothers (51 children), non-supplemented children of allergic mothers (42 children), and non-supplemented children of healthy mothers (28 children) were compared at the age of 6-7 years. A first dose of a probiotic Escherichia coli strain (E. coli O83:K24:H31) was administered within 2 days after the birth and then 12 times during the first months of life and children were followed longitudinally. Proportion and functional properties of Tregs were estimated by flow cytometry in relation to the children's allergy status. Proportion of Tregs in the peripheral blood of children suffering from allergy tends to be higher whereas median of fluorescence intensity (MFI) of FoxP3 was significantly decreased in allergic group. Intracellular presence of regulatory cytokine interleukin (IL)-10 was also lower in allergic children. Immune functions of Tregs reflected by both MFI of FoxP3 and IL-10 in the group of probiotic-supplemented children of allergic mothers were nearly comparable with children of healthy mothers while probiotic non-supplemented children of allergic mothers have decreased immune function of Tregs. Supplementation by probiotic E. coli strain decreases allergy incidence in high-risk children. In contrast to our expectation, proportion of Tregs has not been increased in probiotic supplemented children. Beneficial effect of probiotics on newborn immature immune system could be, at least partially, explained by the modulating immune function of Tregs. In summary, we detected increased proportion of Tregs in peripheral blood of allergic children, their functional properties were decreased in comparison with the Tregs of healthy children. A unifying hypothesis for these findings is that Treg numbers

  10. Quantitative Microbial Risk Assessment for Escherichia coli O157 : H7, Salmonella, and Listeria monocytogenes in Leafy Green Vegetables Consumed at Salad Bars

    NARCIS (Netherlands)

    Franz, E.; Tromp, S.O.; Rijgersberg, H.; Fels-Klerx, van der H.J.

    2010-01-01

    Fresh vegetables are increasingly recognized as a source of foodborne outbreaks in many parts of the world. The purpose of this study was to conduct a quantitative microbial risk assessment for Escherichia coli O157:H7, Salmonella, and Listeria monocytogenes infection from consumption of leafy green

  11. Effect of volumetric water content and clover (Trifolium incarnatum) on the survival of Escherichia coli O157:H7 in a soil matrix

    Science.gov (United States)

    Due to the inevitable introduction of zoonotic manure-born human pathogens, such as Escherichia coli O157:H7, into minimally processed, ready-to-eat and organic vegetable production systems via animal manure-based organic fertilizer, studies aimed at understanding the survival dynamics of these path...

  12. Effect of X-ray treatments on Escherichia coli 0157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes

    Science.gov (United States)

    The aims of this investigation were to; (i) study the effect of X-ray treatments in reducing Escherichia coli O157:H7, Listeria monocytogenes, Salmonella enterica and Shigella flexneri on whole mangoes, and (ii) study the effect of Xray treatments on microflora counts (mesophilic counts, psychrotrop...

  13. Photothermal measurements of high T/sub c/ superconductors

    International Nuclear Information System (INIS)

    Fanton, J.T.; Mitzi, D.B.; Kapitulnik, A.; Khuri-Yakub, B.T.; Kino, G.S.; Gazit, D.; Feigelson, R.S.; Center for Materials Research, Stanford University, Stanford, California 94305-4085)

    1989-01-01

    We demonstrate a photothermal method for making point measurements of the thermal conductivities of high T/sub c/ superconductors. Images made at room temperature on polycrystalline materials show the thermal inhomogeneities. Measurements on single-crystal Bi 2 Sr 2 CaCu 2 O/sub x/ compounds reveal a very large anisotropy of about 7:1 in the thermal conductivity

  14. IL-7 and CCL19 expression in CAR-T cells improves immune cell infiltration and CAR-T cell survival in the tumor.

    Science.gov (United States)

    Adachi, Keishi; Kano, Yosuke; Nagai, Tomohiko; Okuyama, Namiko; Sakoda, Yukimi; Tamada, Koji

    2018-04-01

    Infiltration, accumulation, and survival of chimeric antigen receptor T (CAR-T) cells in solid tumors is crucial for tumor clearance. We engineered CAR-T cells to express interleukin (IL)-7 and CCL19 (7 × 19 CAR-T cells), as these factors are essential for the maintenance of T-cell zones in lymphoid organs. In mice, 7 × 19 CAR-T cells achieved complete regression of pre-established solid tumors and prolonged mouse survival, with superior anti-tumor activity compared to conventional CAR-T cells. Histopathological analyses showed increased infiltration of dendritic cells (DC) and T cells into tumor tissues following 7 × 19 CAR-T cell therapy. Depletion of recipient T cells before 7 × 19 CAR-T cell administration dampened the therapeutic effects of 7 × 19 CAR-T cell treatment, suggesting that CAR-T cells and recipient immune cells collaborated to exert anti-tumor activity. Following treatment of mice with 7 × 19 CAR-T cells, both recipient conventional T cells and administered CAR-T cells generated memory responses against tumors.

  15. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

    2009-02-24

    A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

  16. Use of ionizing radiation in elaborated products of chicken (nuggets) for control of Escherichia coli O157:H7 and salmonella enteriditis

    International Nuclear Information System (INIS)

    Kaempffer Ramirez, Daniela Andrea

    2005-01-01

    The application of ionizing energy in Chicken's Nugget of a trade mark, was studied by the University Santo Tomas in conjunction with the Chilean Nuclear Energy Commission in order to eliminate pathogens such as Escherichia coli and Salmonella enteritidis, in addition to 9 nuggets without sterilize select for RAM. Furthermore, to search the organoleptic characteristic and to Almost Chemist Analysis by means of determined doses. A total of 144 frozen Nuggets (-18 o C) were analyzed and divided into two equal groups for artificially contamination. Each Nuggets - weighting 25 g - was put into sealed polyetilene bags. The two sample groups were sterilized with an irradiation doses of 25 kGy, then inoculated with Escherichia coli O157:H7 strain ATCC 25922 ISP (Instituto de Salud Publica) and Salmonella enteritidis strain ATCC 1833-99 ISP. The samples of each group were treated with gamma irradiation (Co 60 ), with doses of 0, 0.3,0.6 and 0.9 kGy analyzing the bacteria counts after 24 hours, 30 nd 60 days post radiation. D 10 values mid-point were found with a 0,242 kGy for the Escherichia coli and 0,295 kGy for the Salmonella enteritidis. The storage time did not time exert any influence on the D 10 values. The storage time don't showed meaningful differences between the days 1, 30 and 60, in the results obtained in the mid-point D 10 value. The sensory analysis of Nugget was done by means of a trained sensorial panel who evaluated samples with 0; 0.75 and 1,5 kGy. Each person tasted the complete sample (25 g.) and evaluated; appearance, color, odor, , bitterness, texture, flavor and acceptability. Statistically, none attribute showed significant differences (p≤0.05) between the radiated samples and the control group, concluding that the level of the Nugget acceptability was qualified as very good. The Almost Chemist Analysis of Nugget was done to two groups: A control Group (without to irradiate) and a irradiated group with 1.5 kGy. It's evaluated Proteins, Fats

  17. Novel chitosan film embedded with liposome-encapsulated phage for biocontrol of Escherichia coli O157:H7 in beef.

    Science.gov (United States)

    Cui, Haiying; Yuan, Lu; Lin, Lin

    2017-12-01

    In recent years, phages used for the reduction of pathogenic bacteria have fostered many attentions, but they are liable to lost bioactivity in food due to the presence of acidic compounds, enzymes and evaporite materials. To improve the stability of phages, a chitosan edible film containing liposome-encapsulated phage was engineered in the present study. The characteristics of liposome-encapsulated phage and the chitosan film containing liposome-encapsulated phage were investigated. The encapsulation efficiency of phages in liposome reached 57.66±0.12%. Besides, the desirable physical properties of chitosan film were obtained. The chitosan film embedded with liposome-encapsulated phage exhibited high antibacterial activity against Escherichia coli O157:H7, without the impact on the sensory properties of beef. Hence, chitosan film containing liposome-encapsulated phage could be a promising antibacterial packaging for beef preservation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri.

    Science.gov (United States)

    Kabanova, Anastasia; Shneider, Mikhail; Bugaeva, Eugenia; Ha, Vo Thi Ngoc; Miroshnikov, Kirill; Korzhenkov, Aleksei; Kulikov, Eugene; Toschakov, Stepan; Ignatov, Alexander; Miroshnikov, Konstantin

    2018-02-08

    Bacteriophage vB_PpaP_PP74 (PP74) is a novel virulent phage that infects members of the species Pectobacterium parmentieri, a newly established species of soft-rot-causing bacteria in the family Pectobacteriaceae, derived from potato-specific Pectobacterium wasabiae. vB_PpaP_PP74 was identified as a member of the family Podoviridae by transmission electron microscopy. The phage has a 39,790-bp dsDNA genome containing 50 open reading frames (ORFs). Because of the absence of genes encoding toxins or lysogeny factors, PP74 may be considered a candidate phage for pathogen biocontrol applications. The genome layout is similar to genomes of T7-like phages within the subfamily Autographivirinae, and therefore, functions can be attributed to most of ORFs. However, the closest nucleotide sequence homologs of phage PP74 are unclassified Escherichia phages. Based on phylogenetic analysis, vB_PpaP_PP74 is a sensu lato T7-like phage, but it forms a distant subgenus group together with homologous enterobacterial phages.

  19. P2X7 on mouse T cells: one channel, many functions

    Directory of Open Access Journals (Sweden)

    Björn eRissiek

    2015-05-01

    Full Text Available The P2X7 receptor is an adenosine triphosphate (ATP-gated cation channel that is expressed by several cells of the immune system. P2X7 is best known for its proinflammatory role in promoting inflammasome formation and release of mature IL-1β by innate immune cells. Mounting evidence indicates that P2X7 is also an important regulatory receptor of murine and human T cell functions. Murine T cells express a sensitive splice variant of P2X7 that can be activated either by non-covalent binding of ATP or, in the presence of nicotinamide adenine dinucleotide (NAD+, by its covalent ADP-ribosylation catalyzed by the ecto-ADP-ribosyltransferase ARTC2.2. Prolonged activation of P2X7 by either one of these pathways triggers the induction of T cell death. Conversely, lower concentrations of ATP can activate P2X7 to enhance T cell proliferation and production of IL-2. In this review we will highlight the molecular and cellular consequences of P2X7 activation on mouse T cells and its versatile role in T cell homeostasis and activation. Further, we will discuss important differences in the function of P2X7 on human and murine T cells.

  20. Determinação de parâmetros cinéticos da inativação térmica de Escherichia coli em lodo de esgoto Determining kinetic parameters for thermal inactivation of Escherichia coli in sewage sludge

    Directory of Open Access Journals (Sweden)

    Odinei Fogolari

    2012-09-01

    Full Text Available O presente trabalho objetivou determinar parâmetros cinéticos da inativação térmica de Escherichia coli em lodo de esgoto. Os ensaios foram realizados em laboratório pelo método do frasco de três bocas nas temperaturas de 45, 50, 55, 60 e 65ºC. Os resultados indicaram que a cinética de inativação térmica deste microrganismo pode ser descrita por um modelo de primeira ordem. A resistência da bactéria é reduzida consideravelmente em temperaturas acima de 55ºC. A energia de inativação encontrada foi 2,48x10(5 J.mol-1. O tempo de redução decimal D55ºC foi de 3,61 minutos e o coeficiente térmico z foi 8,3ºC.The present study aimed to determine the kinetic parameters of thermal inactivation of Escherichia coli in sewage sludge. The tests were performed in the laboratory using the three-neck flask method at temperatures of 45, 50, 55, 60 and 65ºC. The results indicated that the thermal inactivation kinetic of this microorganism can be described by a first order model. The resistance of bacteria is greatly reduced at temperatures above 55ºC. The inactivation energy was found 2.48x10(5 J.mol-1. The decimal reduction time D55ºC was 3.61 minutes and the thermal coefficient z was 8.3ºC.

  1. Fate of Escherichia coli O157:H7 and Salmonella in soil and lettuce roots as affected by potential home gardening practices.

    Science.gov (United States)

    Erickson, Marilyn C; Liao, Jean; Payton, Alison S; Webb, Cathy C; Ma, Li; Zhang, Guodong; Flitcroft, Ian; Doyle, Michael P; Beuchat, Larry R

    2013-12-01

    The survival and distribution of enteric pathogens in soil and lettuce systems were investigated in response to several practices (soil amendment supplementation and reduced watering) that could be applied by home gardeners. Leaf lettuce was grown in manure compost/top soil (0:5, 1:5 or 2:5 w/w) mixtures. Escherichia coli O157:H7 or Salmonella was applied at a low or high dose (10(3) or 10(6) colony-forming units (CFU) mL(-1) ) to the soil of seedlings and mid-age plants. Supplementation of top soil with compost did not affect pathogen survival in the soil or on root surfaces, suggesting that nutrients were not a limiting factor. Salmonella populations on root surfaces were 0.7-0.8 log CFU g(-1) lower for mid-age plants compared with seedlings. E. coli O157:H7 populations on root surfaces were 0.8 log CFU g(-1) lower for mid-age plants receiving 40 mL of water compared with plants receiving 75 mL of water on alternate days. Preharvest internalization of E. coli O157:H7 and Salmonella into lettuce roots was not observed at any time. Based on the environmental conditions and high pathogen populations in soil used in this study, internalization of Salmonella or E. coli O157:H7 into lettuce roots did not occur under practices that could be encountered by inexperienced home gardeners. © 2013 Society of Chemical Industry.

  2. Antibacterial activities of wasabi against Escherichia coli O157:H7 and Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Zhongjing Lu

    2016-09-01

    Full Text Available Escherichia coli O157:H7 and Staphylococcus aureus are two of the major pathogens frequently involved in foodborne outbreaks. Control of these pathogens in foods is essential to food safety. It is of great interest in the use of natural antimicrobial compounds present in edible plants to control foodborne pathogens as consumers prefer more natural green foods. Allyl isothiocyanate (AITC is an antimicrobial compound naturally present in wasabi (Japanese horseradish and several other edible plants. Although the antibacterial effects of pure AITC and wasabi extract (essential oil against several bacteria have been reported, the antibacterial property of natural wasabi has not been well studied. This study investigated the antibacterial activities of wasabi as well as AITC against E. coli O157:H7 and S. aureus. Chemical analysis showed that AITC is the major isothiocyanate in wasabi. The AITC concentration in the wasabi powder used in this study was 5.91±0.59 mg/g. The minimum inhibitory concentration (MIC of wasabi against E. coli O157:H7 or S. aureus was 1% (or 10 mg/ml. Wasabi at 4% displayed higher bactericidal activity against S. aureus than against E. coli O157:H7. The MIC of AITC against either pathogen was between 10 and 100 µg/ml. AITC at 500 µg/ml was bactericidal against both pathogens while AITC at 1000 µg/ml eliminated E. coli O157:H7 much faster than S. aureus. The results from this study showed that wasabi has strong antibacterial property and has high potential to effectively control E. coli O157:H7 and S. aureus in foods. The antibacterial property along with its natural green color, unique flavor, and advantage to safeguard foods at the point of ingestion makes wasabi a promising natural edible antibacterial plant. The results from this study may be of significant interest to the food industry as they develop new and safe foods. These results may also stimulate more research to evaluate the antibacterial effect of wasabi

  3. Antibacterial Activities of Wasabi against Escherichia coli O157:H7 and Staphylococcus aureus.

    Science.gov (United States)

    Lu, Zhongjing; Dockery, Christopher R; Crosby, Michael; Chavarria, Katherine; Patterson, Brett; Giedd, Matthew

    2016-01-01

    Escherichia coli O157:H7 and Staphylococcus aureus are two of the major pathogens frequently involved in foodborne outbreaks. Control of these pathogens in foods is essential to food safety. It is of great interest in the use of natural antimicrobial compounds present in edible plants to control foodborne pathogens as consumers prefer more natural "green" foods. Allyl isothiocyanate (AITC) is an antimicrobial compound naturally present in wasabi (Japanese horseradish) and several other edible plants. Although the antibacterial effects of pure AITC and wasabi extract (essential oil) against several bacteria have been reported, the antibacterial property of natural wasabi has not been well studied. This study investigated the antibacterial activities of wasabi as well as AITC against E . coli O157:H7 and S . aureus . Chemical analysis showed that AITC is the major isothiocyanate in wasabi. The AITC concentration in the wasabi powder used in this study was 5.91 ± 0.59 mg/g. The minimum inhibitory concentration (MIC) of wasabi against E. coli O157:H7 or S. aureus was 1% (or 10 mg/ml). Wasabi at 4% displayed higher bactericidal activity against S. aureus than against E. coli O157:H7. The MIC of AITC against either pathogen was between 10 and 100 μg/ml. AITC at 500 μg/ml was bactericidal against both pathogens while AITC at 1000 μg/ml eliminated E. coli O157:H7 much faster than S. aureus . The results from this study showed that wasabi has strong antibacterial property and has high potential to effectively control E. coli O157:H7 and S. aureus in foods. The antibacterial property along with its natural green color, unique flavor, and advantage to safeguard foods at the point of ingestion makes wasabi a promising natural edible antibacterial plant. The results from this study may be of significant interest to the food industry as they develop new and safe foods. These results may also stimulate more research to evaluate the antibacterial effect of wasabi against other

  4. The hand: MR imaging with a 4.7-T magnet

    International Nuclear Information System (INIS)

    Wang, P.C.; Archer, A.; Rajan, S.; Carvlin, M.J.; Mun, S.K.; Nelson, M.C.

    1987-01-01

    MR images of normal and pathologic human hands were obtained using a 4.7-T magnet Varian system. Standard spin-echo techniques and inversion-recovery sequences were used to produce both T1- and T2-weighted images. The higher gradient (2 gauss/cm) of the 4.7-T system allows submillimeter resolution. A specially designed surface coil is used to improve the signal-to-noise ratio. The coil is elliptical and measures 3 inches by 4.5 inches. Axial, coronal, and sagittal images were obtained, revealing fine, detailed structures of the human hand. The joint capsule, ligaments and tendons, and vascular structures were clearly visible. The authors will show images of the normal anatomy of the hand, as well as pathologic lesions of inflammatory and crystalline arthropathy. Techniques and special problems of imaging the human hand with a 4.7-T system are discussed

  5. [Virulence markers of Escherichia coli O1 strains].

    Science.gov (United States)

    Makarova, M A; Kaftyreva, L A; Grigor'eva, N S; Kicha, E V; Lipatova, L A

    2011-01-01

    To detect virulence genes in clinical isolates of Escherichia coli O1 using polymerase chain reaction (PCR). One hundred and twenty strains of E.coli O1 strains isolated from faeces of patients with acute diarrhea (n = 45) and healthy persons (n = 75) were studied. PCR with primers for rfb and fliC genes, which control synthesis of O- and H- antigens respectively, was used. Fourteen virulence genes (pap, aaf, sfa, afa, eaeA, bfpA, ial, hly, cnf, stx1, stx2, lt, st, and aer) were detected by PCR primers. K1-antigen was determined by Pastorex Meningo B/E. coli O1 kit (Bio-Rad). rfb gene controlling O-antigen synthesis in serogroup O1 as well as fliC gene controlling synthesis of H7 and K1 antigens were detected in all strains. Thus all E. coli strains had antigenic structure O1:K1 :H-:F7. Virulence genes aafl, sfa, afa, eaeA, bfpA, ial, hly, cnf, stx1, stx2, lt, and st were not detected. All strains owned pap and aer genes regardless of the presence of acute diarrhea symptoms. It was shown that E. coli O1:KI:H-:F7 strains do not have virulence genes which are characteristic for diarrhea-causing Escherichia. In accordance with the presence of pap and aer genes they could be attributed to uropathogenic Escherichia (UPEC) or avian-pathogenic Escherichia (APEC). It is necessary to detect virulence factors in order to determine E. coli as a cause of intestinal infection.

  6. Fate of Escherichia coli O157:H7 (ECOH) in blade tenderized beef prime rib following searing, cooking and holding under commercial conditions

    Science.gov (United States)

    Undercooked non-intact beef has caused a number of illnesses due to contamination with serotype O157:H7 strains of Escherichia coli (ECOH). Few studies have quantified translocation and/or thermal inactivation of ECOH directly in blade tenderized beef. There have been no such studies for prime rib,...

  7. Investigation of carbon storage regulation network (csr genes) and phenotypic differences between acid sensitive and resistant Escherichia coli O157:H7 strains

    Science.gov (United States)

    Background: Escherichia coli O157:H7 and related serotype strains have previously been shown to vary in acid resistance, however, little is known about strain specific mechanisms of acid resistance. We examined sensitive and resistant E. coli strains to determine the effects of growth in minimal and...

  8. Accurate measurement of gene copy number for human alpha-defensin DEFA1A3.

    Science.gov (United States)

    Khan, Fayeza F; Carpenter, Danielle; Mitchell, Laura; Mansouri, Omniah; Black, Holly A; Tyson, Jess; Armour, John A L

    2013-10-20

    Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing. In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples. We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn's disease, type I diabetes, HIV progression and multiple sclerosis.

  9. Earthworms as vectors of Escherichia coli O157:H7 in soil and vermicomposts.

    Science.gov (United States)

    Williams, A Prysor; Roberts, Paula; Avery, Lisa M; Killham, Ken; Jones, David L

    2006-10-01

    Survival and movement of Escherichia coli O157:H7 in both soil and vermicompost is of concern with regards to human health. Whilst it is accepted that E. coli O157:H7 can persist for considerable periods in soils, it is not expected to survive thermophilic composting processes. However, the natural behavior of earthworms is increasingly utilized for composting (vermicomposting), and the extent to which earthworms promote the survival and dispersal of the bacterium within such systems is unknown. The faecal material produced by earthworms provides a ready supply of labile organic substrates to surrounding microbes within soil and compost, thus promoting microbial activity. Earthworms can also cause significant movement of organisms through the channels they form. Survival and dispersal of E. coli O157:H7 were monitored in contaminated soil and farmyard manure subjected to earthworm digestion over 21 days. Our findings lead to the conclusion that anecic earthworms such as Lumbricus terrestris may significantly aid vertical movement of E. coli O157 in soil, whereas epigeic earthworms such as Dendrobaena veneta significantly aid lateral movement within compost. Although the presence of earthworms in soil and compost may aid proliferation of E. coli O157 in early stages of contamination, long-term persistence of the pathogen appears to be unaffected.

  10. Prevalence and relatedness of Escherichia coli O157:H7 strains in the feces and on the hides and carcasses of U.S. meat goats at slaughter.

    Science.gov (United States)

    Jacob, M E; Foster, D M; Rogers, A T; Balcomb, C C; Sanderson, M W

    2013-07-01

    We determined the prevalences of Escherichia coli O157:H7 in feces, hide, and carcasses of meat goats at a U.S. processing plant. Prevalences were 11.1%, 2.7%, and 2.7%, respectively. Sixteen pulsed-field gel electrophoresis (PFGE) subtypes were identified among 49 E. coli O157:H7 isolates, some of which were present on multiple sample types or collection days.

  11. Immunological Analysis of Treatment Interruption After Early Highly Active Antiretroviral Therapy

    NARCIS (Netherlands)

    Schellens, Ingrid M. M.; Pogany, Katalin; Westerlaken, Geertje H. A.; Borghans, José A. M.; Miedema, Frank; van Valkengoed, Irene G. M.; Kroon, Frank P.; Lange, Joep M. A.; Brinkman, Kees; Prins, Jan M.; van Baarle, Debbie

    2010-01-01

    We longitudinally evaluated HIV-specific T-cell immunity after discontinuation of highly active antiretroviral therapy (HAART). After treatment interruption (TI), some individuals could maintain a low plasma viral load ( <15,000 copies/mL), whereas others could not (>50,000 copies/mL). Before HAART

  12. Vanillin production using Escherichia coli cells over-expressing isoeugenol monooxygenase of Pseudomonas putida.

    Science.gov (United States)

    Yamada, Mamoru; Okada, Yukiyoshi; Yoshida, Toyokazu; Nagasawa, Toru

    2008-04-01

    The isoeugenol monooxygenase gene of Pseudomonas putida IE27 was inserted into an expression vector, pET21a, under the control of the T7 promoter. The recombinant plasmid was introduced into Escherichia coli BL21(DE3) cells, containing no vanillin-degrading activity. The transformed E. coli BL21(DE3) cells produced 28.3 g vanillin/l from 230 mM isoeugenol, with a molar conversion yield of 81% at 20 degrees C after 6 h. In the reaction system, no accumulation of undesired by-products, such as vanillic acid or acetaldehyde, was observed.

  13. Biofilm production and antibiotic susceptibility profile of Escherichia ...

    African Journals Online (AJOL)

    Samie.Amidou

    2012-04-26

    Apr 26, 2012 ... Full Length Research Paper. Biofilm production and antibiotic susceptibility profile of Escherichia coli isolates from HIV and AIDS patients in the Limpopo Province. Samie, A. and Nkgau, T. F.. Department of Microbiology, University of Venda, Private Bag X5050, Thohoyandou 0950, Limpopo, South Africa.

  14. Prevalence of Escherichia Coli O157:H7 and Enterobacteriaceae on Hands of Workers in Halal Cattle Abattoirs in Peninsular Malaysia.

    Science.gov (United States)

    Shamsul, Bahri Mohd Tamrin; Adamu, Muhammad Tukur; Mohd Desa, Mohd Nasir; Khairani-Bejo, Siti

    2016-09-01

    Several occupational diseases of multiple origins are encountered among abattoir workers. Presence of indicator microorganisms (coliforms) on hands of workers can be used a gauge for hygienic practices. A cross-sectional study was performed to assess the prevalence of E.coli and enterobacteriaceae among Halal abattoir workers in some government halal abattoirs of Malaysia. A total of one hundred and sixty-five hand swab samples were collected from workers of Halal abattoirs in Malaysia. The samples were subjected to microbiological analysis for characterisation and serotyping. The results have shown that no Escherichia coli O157:H7 was isolated on the hands of abattoir workers before and after work. However, a total prevalence of 9.7% was recorded for all samples during work. For non-O157:H7, total prevalence of 33.3% during work and 13% after work were obtained. High prevalence was recorded in sample taken during work from Tampin, Jasin and Kemaman (100% each) while low prevalence where observed in Shah Alam, Banting and Ipoh (20% each). Based on the findings the hygienic practices of hand washing among the workers in few locations was found to be low especially after work.

  15. 7T MRI in focal epilepsy with unrevealing conventional field strength imaging.

    Science.gov (United States)

    De Ciantis, Alessio; Barba, Carmen; Tassi, Laura; Cosottini, Mirco; Tosetti, Michela; Costagli, Mauro; Bramerio, Manuela; Bartolini, Emanuele; Biagi, Laura; Cossu, Massimo; Pelliccia, Veronica; Symms, Mark R; Guerrini, Renzo

    2016-03-01

    To assess the diagnostic yield of 7T magnetic resonance imaging (MRI) in detecting and characterizing structural lesions in patients with intractable focal epilepsy and unrevealing conventional (1.5 or 3T) MRI. We conducted an observational clinical imaging study on 21 patients (17 adults and 4 children) with intractable focal epilepsy, exhibiting clinical and electroencephalographic features consistent with a single seizure-onset zone (SOZ) and unrevealing conventional MRI. Patients were enrolled at two tertiary epilepsy surgery centers and imaged at 7T, including whole brain (three-dimensional [3D] T1 -weighted [T1W] fast-spoiled gradient echo (FSPGR), 3D susceptibility-weighted angiography [SWAN], 3D fluid-attenuated inversion recovery [FLAIR]) and targeted imaging (2D T2*-weighted dual-echo gradient-recalled echo [GRE] and 2D gray-white matter tissue border enhancement [TBE] fast spin echo inversion recovery [FSE-IR]). MRI studies at 1.5 or 3T deemed unrevealing at the referral center were reviewed by three experts in epilepsy imaging. Reviewers were provided information regarding the suspected localization of the SOZ. The same team subsequently reviewed 7T images. Agreement in imaging interpretation was reached through consensus-based discussions based on visual identification of structural abnormalities and their likely correlation with clinical and electrographic data. 7T MRI revealed structural lesions in 6 (29%) of 21 patients. The diagnostic gain in detection was obtained using GRE and FLAIR images. Four of the six patients with abnormal 7T underwent epilepsy surgery. Histopathology revealed focal cortical dysplasia (FCD) in all. In the remaining 15 patients (71%), 7T MRI remained unrevealing; 4 of the patients underwent epilepsy surgery and histopathologic evaluation revealed gliosis. 7T MRI improves detection of epileptogenic FCD that is not visible at conventional field strengths. A dedicated protocol including whole brain FLAIR and GRE images at 7T

  16. Use of T7 RNA polymerase to direct expression of outer Surface Protein A (OspA) from the Lyme disease Spirochete, Borrelia burgdorferi

    Science.gov (United States)

    Dunn, John J.; Lade, Barbara N.

    1991-01-01

    The OspA gene from a North American strain of the Lyme disease Spirochete, Borrelia burgdorferi, was cloned under the control of transciption and translation signals from bacteriophage T7. Full-length OspA protein, a 273 amino acid (31kD) lipoprotein, is expressed poorly in Escherichia coli and is associated with the insoluble membrane fraction. In contrast, a truncated form of OspA lacking the amino-terminal signal sequence which normally would direct localization of the protein to the outer membrane is expressed at very high levels (less than or equal to 100 mg/liter) and is soluble. The truncated protein was purified to homogeneity and is being tested to see if it will be useful as an immunogen in a vaccine against Lyme disease. Circular dichroism and fluorescence spectroscopy was used to characterize the secondary structure and study conformational changes in the protein. Studies underway with other surface proteins from B burgdorferi and a related spirochete, B. hermsii, which causes relapsing fever, leads us to conclude that a strategy similar to that used to express the truncated OspA can provide a facile method for producing variations of Borrelia lipoproteins which are highly expressed in E. coli and soluble without exposure to detergents.

  17. Gene variation in IL-7 receptor (IL-7R)α affects IL-7R response in CD4+ T cells in HIV-infected individuals

    DEFF Research Database (Denmark)

    Hartling, Hans Jakob; Ryder, Lars P.; Ullum, Henrik

    2017-01-01

    Optimal CD4+ T cell recovery after initiating combination antiretroviral treatment (cART) in HIV infection reduces risk of morbidity and mortality. T-allele homozygosity (‘TT’) in the single nucleotide polymorphism, rs6897932(C/T), in the IL-7 receptor α (IL-7RA) is associated with faster CD4+ T...... cell recovery after cART initiation compared to C-allele homozygosity in rs6897932 (‘CC’). However, underlying mechanisms are unknown. We aimed to examine potential mechanisms explaining the association between rs6897932 and CD4+ T cell recovery. Ten ‘TT’ and 10 ‘CC’ HIV-infected individuals matched...... on gender, age, and nadir and current CD4+ T cell counts were included in a cross-sectional study. ‘TT’ individuals had higher proportion of CD4+ T cells expressing pSTAT5 compared to ‘CC’ individuals after stimulating with IL-7, especially when co-stimulated with soluble IL7-RA (sIL-7RA). Furthermore, ‘TT...

  18. Multiple-copy entanglement transformation and entanglement catalysis

    International Nuclear Information System (INIS)

    Duan Runyao; Feng Yuan; Li Xin; Ying Mingsheng

    2005-01-01

    We prove that any multiple-copy entanglement transformation [S. Bandyopadhyay, V. Roychowdhury, and U. Sen, Phys. Rev. A 65, 052315 (2002)] can be implemented by a suitable entanglement-assisted local transformation [D. Jonathan and M. B. Plenio, Phys. Rev. Lett. 83, 3566 (1999)]. Furthermore, we show that the combination of multiple-copy entanglement transformation and the entanglement-assisted one is still equivalent to the pure entanglement-assisted one. The mathematical structure of multiple-copy entanglement transformations then is carefully investigated. Many interesting properties of multiple-copy entanglement transformations are presented, which exactly coincide with those satisfied by the entanglement-assisted ones. Most interestingly, we show that an arbitrarily large number of copies of state should be considered in multiple-copy entanglement transformations

  19. ANALISIS MIKROBIOLOGI ESCHERICHIA COLI O157:H7 PADA HASIL OLAHAN HEWAN SAPI DALAM PROSES PRODUKSINYA

    Directory of Open Access Journals (Sweden)

    Trini Sudiarti

    2005-06-01

    Full Text Available Microbiological analysis of Escherichia coli O157:H7 on Cow’s Products during the Production Process. The problem on food health is the high amount of bacterial contamination of food served by several kinds of food sellers, e.g. vendors, restaurants, caterers and food industries. Meat and milk products are kinds of food prone to contamination. To secure food against contamination by bacteria such as E. coli O157:H7, especially related to raw food, should beginwith the securing of products through the whole production process till it reaches the consumers. Although these pathogenic bacteria are part of the normal flora in the intestines of cattle, however we should be aware of the possibility of an outbreak in the community due to E. coli O157:H7 contamination of beef products. To anticipate the danger of an outbreak a study should be conducted to know about this microorganism from the beginning i.e. the production phaseuntil the seller phase. The aim of this research is to know the existence of E. coli O157:H7 on beef and milk products obtained from abattoirs, cow ranches, traditional markets and other sellers in addition with knowing the influencing factors on the spreading of the microorganism. The survey design used for this research is the cross sectional design. The material used for the tests are 250 ml water/milk and 250 gram beef/carcass. The bacterial tests included qualitative tests as follows: presumptive test, confirmed test, completed test, whereas quantitatively tests as follows: Total PlateCound (TPC, Most Probable Number (MPN, which is a near amount prediction of bacteria per 100 ml of water. Results showed that all meat (100% coming from abattoirs and traditional markets were contaminated with E. coli O157:H7, in addition with most of the fresh and pasteurized milk samples (73.3% coming from cattle ranches and home industries. Contamination was also found in most of the water samples (60% and in food handlers (41.7%.

  20. Phosphorus magnetic resonance spectroscopic imaging at 7 T in patients with prostate cancer.

    Science.gov (United States)

    Lagemaat, Miriam W; Vos, Eline K; Maas, Marnix C; Bitz, Andreas K; Orzada, Stephan; van Uden, Mark J; Kobus, Thiele; Heerschap, Arend; Scheenen, Tom W J

    2014-05-01

    The aim of this study was to identify characteristics of phosphorus (P) spectra of the human prostate and to investigate changes of individual phospholipid metabolites in prostate cancer through in vivo P magnetic resonance spectroscopic imaging (MRSI) at 7 T. In this institutional review board-approved study, 15 patients with biopsy-proven prostate cancer underwent T2-weighted magnetic resonance imaging and 3-dimensional P MRSI at 7 T. Voxels were selected at the tumor location, in normal-appearing peripheral zone tissue, normal-appearing transition zone tissue, and in the base of the prostate close to the seminal vesicles. Phosphorus metabolite ratios were determined and compared between tissue types. Signals of phosphoethanolamine (PE) and phosphocholine (PC) were present and well resolved in most P spectra in the prostate. Glycerophosphocholine signals were observable in 43% of the voxels in malignant tissue, but in only 10% of the voxels in normal-appearing tissue away from the seminal vesicles. In many spectra, independent of tissue type, 2 peaks resonated in the chemical shift range of inorganic phosphate, possibly representing 2 separate pH compartments. The PC/PE ratio in the seminal vesicles was highly elevated compared with the prostate in 5 patients. A considerable overlap of P metabolite ratios was found between prostate cancer and normal-appearing prostate tissue, preventing direct discrimination of these tissues. The only 2 patients with high Gleason scores tumors (≥4+5) presented with high PC and glycerophosphocholine levels in their cancer lesions. Phosphorus MRSI at 7 T shows distinct features of phospholipid metabolites in the prostate gland and its surrounding structures. In this exploratory study, no differences in P metabolite ratios were observed between prostate cancer and normal-appearing prostate tissue possibly because of the partial volume effects of small tumor foci in large MRSI voxels.

  1. Survival, injury and inactivation of Escherichia coli 0157:H7, salmonella and aerobic mesophilic bacteria in apple juice and cider amended with nisin-edta

    Science.gov (United States)

    For health reasons, people are consuming fresh juices or minimally processed fruit and vegetable juices, thereby, exposing themselves to the risk of foodborne illness if such juices are contaminated with bacteria pathogens. Behavior of aerobic mesophilic bacteria, Escherichia coli O157:H7 and Salmon...

  2. Microstrip Butler matrix design and realization for 7 T MRI.

    Science.gov (United States)

    Yazdanbakhsh, Pedram; Solbach, Klaus

    2011-07-01

    This article presents the design and realization of 8 × 8 and 16 × 16 Butler matrices for 7 T MRI systems. With the focus on low insertion loss and high amplitude/phase accuracy, the microstrip line integration technology (microwave-integrated circuit) was chosen for the realization. Laminate material of high permittivity (ε(r) = 11) and large thickness (h = 3.2 mm) is shown to allow the best trade-off of circuit board size versus insertion loss, saving circuit area by extensive folding of branch-line coupler topology and meandering phase shifter and connecting strip lines and reducing mutual coupling of neighboring strip lines by shield structures between strip lines. With this approach, 8 × 8 Butler matrices were produced in single boards of 310 mm × 530 mm, whereas the 16 × 16 Butler matrices combined two submatrices of 8 × 8 with two smaller boards. Insertion loss was found at 0.73 and 1.1 dB for an 8 × 8 matrix and 16 × 16 matrix, respectively. Measured amplitude and phase errors are shown to represent highly pure mode excitation with unwanted modes suppressed by 40 and 35 dB, respectively. Both types of matrices were implemented with a 7 T MRI system and 8- and 16-element coil arrays for RF mode shimming experiments and operated successfully with 8 kW of RF power. Copyright © 2011 Wiley-Liss, Inc.

  3. 26 CFR 1.382-7T - Built-in gains and losses (temporary).

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 4 2010-04-01 2010-04-01 false Built-in gains and losses (temporary). 1.382-7T Section 1.382-7T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Insolvency Reorganizations § 1.382-7T Built-in gains and losses...

  4. Mathematical modeling the cross-contamination of Escherichia coli O157:H7 on the surface of ready-to-eat meat product while slicing

    Science.gov (United States)

    Microbial cross-contamination either at home or production site is one of the major factors of causing contamination of foods and leading to the foodborne illness. The knowledge regarding Escherichia coli O157:H7 surface transfer on ready-to-eat (RTE) deli meat and the slicer used for slicing diffe...

  5. Genome and Plasmid Sequences of Escherichia coli KV7, an Extended-Spectrum β-Lactamase Isolate Derived from Feces of a Healthy Pig

    DEFF Research Database (Denmark)

    Bateman, Michael D; de Vries, Stefan P W; Gupta, Srishti

    2017-01-01

    We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27, phylogenetic group D) and its six plasmids, isolated from a healthy pig, as determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of 4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-...

  6. Frequency and risk-factors analysis of Escherichia coli O157:H7 in Bali-cattle.

    Science.gov (United States)

    Suardana, I Wayan; Widiasih, Dyah Ayu; Nugroho, Widagdo Sri; Wibowo, Michael Haryadi; Suyasa, I Nyoman

    2017-08-01

    Cattle are known as the main reservoir of zoonotic agents verocytotoxin-producing Escherichia coli. These bacteria are usually isolated from calves with diarrhea and/or mucus and blood. Tolerance of these agents to the environmental conditions will strengthen of their transmission among livestock. A total of 238 cattle fecal samples from four sub-districts in Badung, Bali were used in this study. Epidemiological data observed include cattle age, sex, cattle rearing system, the source of drinking water, weather, altitude, and type of cage floor, the cleanliness of cage floor, the slope of cage floor, and the level of cattle cleanliness. The study was initiated by culturing of samples onto eosin methylene blue agar, then Gram stained, and tested for indole, methyl-red, voges proskauer, and citrate, Potential E.coli isolates were then cultured onto sorbitol MacConkey agar, and further tested using O157 latex agglutination test and H7 antisera. Molecular identification was performed by analysis of the 16S rRNA gene, and epidemiological data was analyzed using STATA 12.0 software. The results showed, the prevalence of E. coli O157:H7 in cattle at Badung regency was 6.30% (15/238) covering four sub districts i.e. Petang, Abiansemal, Mengwi, and Kuta which their prevalence was 8.62%(5/58), 10%(6/60), 3.33%(2/60), and 3.33(2/60)%, respectively. The analysis of 16S rRNA gene confirmed of isolates as an E. coli O157:H7 strain with 99% similarities. Furthermore, the risk factors analysis showed that the slope of the cage floor has a highly significant effect (P<0.05) to the distribution of infection. Consequently, implementing this factor must be concerned in order to decrease of infection. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Efficacy of (+-Lariciresinol to Control Bacterial Growth of Staphylococcus aureus and Escherichia coli O157:H7

    Directory of Open Access Journals (Sweden)

    Vivek K. Bajpai

    2017-05-01

    Full Text Available This study was undertaken to assess the antibacterial potential of a polyphenolic compound (+-lariciresinol isolated from Rubia philippinensis against selected foodborne pathogens Staphylococcus aureus KCTC1621 and Escherichia coli O157:H7. (+-Lariciresinol at the tested concentrations (250 μg/disk evoked a significant antibacterial effect as a diameter of inhibition zones (12.1–14.9 mm with minimum inhibitory concentration (MIC, and minimum bactericidal concentration values of 125–250 and 125–250 μg/mL, respectively. Furthermore, (+-lariciresinol at MIC showed reduction in bacterial cell viabilities, efflux of potassium (K+ ions and release of 260 nm materials against E. coli O157:H7 and S. aureus KCTC1621. Moreover, deteriorated cell wall morphology of E. coli O157:H7 and S. aureus KCTC1621 cells treated with (+-lariciresinol at MIC further confirmed its inhibitory effect against the tested pathogens, suggesting it to be an alternative means of antimicrobials.

  8. Detection of Escherichia coli O157:H7 and Salmonella in ground beef by a bead-free quantum dot-facilitated isolation method.

    Science.gov (United States)

    Wang, Luxin; Wu, Chung-Shieh; Fan, Xudong; Mustapha, Azlin

    2012-05-01

    The aims of this study were to introduce a new immunological bead-free cell detection method using quantum dots (QDs) as reporter markers for foodborne pathogen detection. QDs are nanosized particles with long-term photostability, high quantum yield, broad absorption spectra, and narrow, symmetric emission and high signal-to-noise ratio. The chemical compound [(1-ethyl-3-3-dimethylaminopropyl) carbodiimide hydrochloride] (EDC) and protein A were used as crosslinkers for manufacturing QD-antibody conjugates. To minimize the inhibition of QD fluorescence by the magnetic beads, the beads were removed after the primary pathogen isolation and before fluorescence measurement. Detection signals were increased four-fold after employing the bead-free isolation method. With a 24-h enrichment, the bead-free QD-facilitated detection method was able to detect 10 CFU/g Escherichia coli O157:H7 and Salmonella from artificially contaminated ground beef. To our knowledge, this detection method is the first research that combined a new EDC-protein A QD-labeling technique and bead-free fluorescence measurement to detect E. coli O157:H7 and Salmonella in ground beef. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Ballistic Limit of High-Strength Steel and Al7075-T6 Multi-Layered Plates Under 7.62-mm Armour Piercing Projectile Impact

    OpenAIRE

    Rahman, N. A.; Abdullah, S.; Zamri, W. F. H.; Abdullah, M. F.; Omar, M. Z.; Sajuri, Z.

    2016-01-01

    Abstract This paper presents the computational-based ballistic limit of laminated metal panels comprised of high strength steel and aluminium alloy Al7075-T6 plate at different thickness combinations to necessitate the weight reduction of existing armour steel plate. The numerical models of monolithic configuration, double-layered configuration and triple-layered configuration were developed using a commercial explicit finite element code and were impacted by 7.62 mm armour piercing projectil...

  10. Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T.

    Science.gov (United States)

    Beaujoin, Justine; Palomero-Gallagher, Nicola; Boumezbeur, Fawzi; Axer, Markus; Bernard, Jeremy; Poupon, Fabrice; Schmitz, Daniel; Mangin, Jean-François; Poupon, Cyril

    2018-06-01

    The human hippocampus plays a key role in memory management and is one of the first structures affected by Alzheimer's disease. Ultra-high magnetic resonance imaging provides access to its inner structure in vivo. However, gradient limitations on clinical systems hinder access to its inner connectivity and microstructure. A major target of this paper is the demonstration of diffusion MRI potential, using ultra-high field (11.7 T) and strong gradients (750 mT/m), to reveal the extra- and intra-hippocampal connectivity in addition to its microstructure. To this purpose, a multiple-shell diffusion-weighted acquisition protocol was developed to reach an ultra-high spatio-angular resolution with a good signal-to-noise ratio. The MRI data set was analyzed using analytical Q-Ball Imaging, Diffusion Tensor Imaging (DTI), and Neurite Orientation Dispersion and Density Imaging models. High Angular Resolution Diffusion Imaging estimates allowed us to obtain an accurate tractography resolving more complex fiber architecture than DTI models, and subsequently provided a map of the cross-regional connectivity. The neurite density was akin to that found in the histological literature, revealing the three hippocampal layers. Moreover, a gradient of connectivity and neurite density was observed between the anterior and the posterior part of the hippocampus. These results demonstrate that ex vivo ultra-high field/ultra-high gradients diffusion-weighted MRI allows the mapping of the inner connectivity of the human hippocampus, its microstructure, and to accurately reconstruct elements of the polysynaptic intra-hippocampal pathway using fiber tractography techniques at very high spatial/angular resolutions.

  11. Synthesis of highly water-soluble fluorescent conjugated glycopoly(p-phenylene)s for lectin and Escherichia coli.

    Science.gov (United States)

    Xue, Cuihua; Jog, Sonali P; Murthy, Pushpalatha; Liu, Haiying

    2006-09-01

    Two facile, convenient, and versatile synthetic approaches are used to covalently attach carbohydrate residues to conjugated poly(p-phenylene)s (PPPs) for highly water-soluble PPPs bearing alpha-mannopyranosyl and beta-glucopyranosyl pendants (polymers A and B), which highly fluoresce in phosphate buffer (pH 7.0). The post-polymerization functionalization approach is to treat bromo-bearing PPP (polymer 1) with 1-thiolethyl-alpha-D-mannose tetraacetate or 1-thiol-beta-D-glucose tetraacetate in THF solution in the presence of K(2)CO(3) at room temperature through formation of thioether bridges, affording polymer 2a or 2b. The prepolymerization functionalization approach is to polymerize a well-defined sugar-carrying monomer, affording polymer 2a. Polymers 2a and 2b were deacetylated under Zemplén conditions in methanol and methylene chloride containing sodium methoxide, affording polymers A and B, respectively. The multivalent display of carbohydrates on the fluorescent conjugated glycopolymer overcomes the characteristic low binding affinity of the individual carbohydrates to their receptor proteins. Titration of concanavalin A (Con A) to alpha-mannose-bearing polymer A resulted in significant fluorescent quenching of the polymer with Stern-Volmer quenching constant of 4.5 x 10(7). Incubation of polymer A with Escherichia coli (E. coli) lead to formation of fluorescently stained bacterial clusters. Beta-glucose-bearing polymer B displayed no response to Con A and E. coli.

  12. Aqueous corrosion mechanisms of the nuclear glass R7T7. Experimental approach. Kinetics and thermodynamic simulation

    International Nuclear Information System (INIS)

    Advocat, T.

    1991-01-01

    An inactive borosilicate glass made of about 30 oxides is studied. The composition was developed by the CEA for encapsulation of calcinated fission product solutions from reprocessing. Hydration energy of glass is first calculated for 8 glasses and results are compared to experimental data. Dissolution of R7T7 glass is examined at 90 0 C in a large range of pH and S/V ratios (glass surface/solution volume). In dilute media (S/V = 0.1 cm -1 ) dissolution is selective at acid pH and stoichiometric at basic pH. In alkaline media dissolution rate increases with pH. Corrosion products, generally amorphous or badly crystallized are observed on glass surface. For high S/V ratios (4, 20, 80 and 200 cm -1 ) the very low dissolution rate is explained by saturation. Orthosilic acid controls corrosion kinetics. A kinetic equation is proposed taking into account pH, S/V ratio and dissolved silica concentration. Geochemical consequences of R7T7 dissolution are modelled at 100 0 C and 90 0 C. Affinity of dissolution reaction depends upon many factors (pH, silica concentration, nature and crystallinity of secondary phases. Reaction affinity is not constant for the long-term [fr

  13. DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

    Directory of Open Access Journals (Sweden)

    Jackson Stuart

    2010-04-01

    Full Text Available Abstract Background DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. Results We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. Conclusion The described assay outputs absolute copy number, outputs an error estimate (p-value, and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.

  14. Effect of x-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes

    Science.gov (United States)

    The aims of this investigation were to; (i) study the effect of X-ray treatments in reducing Escherichia coli O157:H7, Listeria monocytogenes, Salmonella enterica and Shigella flexneri on whole mangoes, and (ii) study the effect of Xray treatments on microflora counts (mesophilic counts, psychrotrop...

  15. Hard Copy Market Overview

    Science.gov (United States)

    Testan, Peter R.

    1987-04-01

    A number of Color Hard Copy (CHC) market drivers are currently indicating strong growth in the use of CHC technologies for the business graphics marketplace. These market drivers relate to product, software, color monitors and color copiers. The use of color in business graphics allows more information to be relayed than is normally the case in a monochrome format. The communicative powers of full-color computer generated output in the business graphics application area will continue to induce end users to desire and require color in their future applications. A number of color hard copy technologies will be utilized in the presentation graphics arena. Thermal transfer, ink jet, photographic and electrophotographic technologies are all expected to be utilized in the business graphics presentation application area in the future. Since the end of 1984, the availability of color application software packages has grown significantly. Sales revenue generated by business graphics software is expected to grow at a compound annual growth rate of just over 40 percent to 1990. Increased availability of packages to allow the integration of text and graphics is expected. Currently, the latest versions of page description languages such as Postscript, Interpress and DDL all support color output. The use of color monitors will also drive the demand for color hard copy in the business graphics market place. The availability of higher resolution screens is allowing color monitors to be easily used for both text and graphics applications in the office environment. During 1987, the sales of color monitors are expected to surpass the sales of monochrome monitors. Another major color hard copy market driver will be the color copier. In order to take advantage of the communications power of computer generated color output, multiple copies are required for distribution. Product introductions of a new generation of color copiers is now underway with additional introductions expected

  16. Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation.

    Science.gov (United States)

    E, Chao; Duan, Baogen; Yu, Jin

    2017-04-20

    Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection. We calculated the relative binding free energy between a noncognate nucleotide and a cognate one at a preinsertion configuration via alchemical simulations, showing that a small selection free energy or the binding free energy difference (∼3 k B T) exists between the two nucleotides. Indeed, another preinsertion configuration favored by the noncognate nucleotides was identified, which appears to be off path for further nucleotide insertion and additionally assists the nucleotide selection. By chemical master equation (CME) approach, we show that the small selection free energy at the preinsertion site along with the off-path noncognate nucleotide filtering can help substantially to reduce the error rate and to maintain the elongation rate high in the T7 RNAP transcription.

  17. A new sulfonamide resistance gene (sul3) in Escherichia coli is widespread in the pig population of Switzerland.

    Science.gov (United States)

    Perreten, Vincent; Boerlin, Patrick

    2003-03-01

    A new gene, sul3, which specifies a 263-amino-acid protein similar to a dihydropteroate synthase encoded by the 54-kb conjugative plasmid pVP440 from Escherichia coli was characterized. Expression of the cloned sul3 gene conferred resistance to sulfamethoxazole on E. coli. Two copies of the insertion element IS15Delta/26 flanked the region containing sul3. The sul3 gene was detected in one-third of the sulfonamide-resistant pathogenic E. coli isolates from pigs in Switzerland.

  18. A New Sulfonamide Resistance Gene (sul3) in Escherichia coli Is Widespread in the Pig Population of Switzerland

    OpenAIRE

    Perreten, Vincent; Boerlin, Patrick

    2003-01-01

    A new gene, sul3, which specifies a 263-amino-acid protein similar to a dihydropteroate synthase encoded by the 54-kb conjugative plasmid pVP440 from Escherichia coli was characterized. Expression of the cloned sul3 gene conferred resistance to sulfamethoxazole on E. coli. Two copies of the insertion element IS15Δ/26 flanked the region containing sul3. The sul3 gene was detected in one-third of the sulfonamide-resistant pathogenic E. coli isolates from pigs in Switzerland.

  19. PCR and ELISA (VIDAS ECO O157® Escherichia coli O157:H7 identification in Minas Frescal cheese commercialized in Goiânia, GO

    Directory of Open Access Journals (Sweden)

    Rosangela Nunes Carvalho

    2014-01-01

    Full Text Available Escherichia coli O157:H7 has been incriminated in food poisoning outbreaks and sporadic cases of hemorrhagic colitis and hemolytic uremic syndrome in many countries. Considering the high susceptibility of Minas Frescal cheese to contamination by E. coli O157:H7, the aim of this study was to determine the occurrence of this pathogen through PCR (Polymerase Chain Reaction and ELISA (VIDAS ECO O157®, bioMérieux, Lyon, France test. Thirty cheese samples manufactured by artisan farmhouse producers were collected from open-air markets in Goiânia and thirty from industries under Federal Inspection located in Goiás State which trade their products in supermarkets in Goiânia. E. coli O157:H7 was detected in 6.67% samples collected in open air markets using ELISA, and 23,33% with PCR. The pathogen was not detected in samples from industries under Federal Inspection.

  20. PCR and ELISA (VIDAS ECO O157®) Escherichia coli O157:H7 identification in Minas Frescal cheese commercialized in Goiânia, GO

    Science.gov (United States)

    Carvalho, Rosangela Nunes; de Oliveira, Antonio Nonato; de Mesquita, Albenones José; Minafra e Rezende, Cíntia Silva; de Mesquita, Adriano Queiroz; Romero, Rolando Alfredo Mazzoni

    2014-01-01

    Escherichia coli O157:H7 has been incriminated in food poisoning outbreaks and sporadic cases of hemorrhagic colitis and hemolytic uremic syndrome in many countries. Considering the high susceptibility of Minas Frescal cheese to contamination by E. coli O157:H7, the aim of this study was to determine the occurrence of this pathogen through PCR (Polymerase Chain Reaction) and ELISA (VIDAS ECO O157®, bioMérieux, Lyon, France) test. Thirty cheese samples manufactured by artisan farmhouse producers were collected from open-air markets in Goiânia and thirty from industries under Federal Inspection located in Goiás State which trade their products in supermarkets in Goiânia. E. coli O157:H7 was detected in 6.67% samples collected in open air markets using ELISA, and 23,33% with PCR. The pathogen was not detected in samples from industries under Federal Inspection. PMID:24948907

  1. Radiocomplexation and evaluation of the 99mTc-Gemifloxacin in artificially Escherichia coli infected mice

    International Nuclear Information System (INIS)

    Erfani, M.; Shafiei, M.; Rekabgardan, M.; Mortazavi, P.

    2016-01-01

    Gemifloxacin as a broad spectrum quinolone antibacterial agent was radiocomplexed with high activity of 99m Tc and was evaluated as an infection imaging agent in artificially Escherichia coli (E. Coli) infected mice. 99m Tc-Gemifloxacin with high specific activity (0.148 GBq/μmol) and labeling yield (98.60 ± 0.70 %) was obtained. Our main achievement was high accumulation in the E. Coli infected right thigh muscle in mice (T/NT = 1.89 at 4 h post injection) which may diagnostically be beneficial to distinguish sites of E. Coli infection. (author)

  2. Prognostic and predictive values of EGFR overexpression and EGFR copy number alteration in HER2-positive breast cancer.

    Science.gov (United States)

    Lee, H J; Seo, A N; Kim, E J; Jang, M H; Kim, Y J; Kim, J H; Kim, S-W; Ryu, H S; Park, I A; Im, S-A; Gong, G; Jung, K H; Kim, H J; Park, S Y

    2015-01-06

    Epidermal growth factor receptor (EGFR) is overexpressed in a subset of human epidermal growth factor receptor 2 (HER2)-positive breast cancers, and coexpression of HER2 and EGFR has been reported to be associated with poor clinical outcome. Moreover, interaction between HER2 and EGFR has been suggested to be a possible basis for trastuzumab resistance. We analysed the clinical significance of EGFR overexpression and EGFR gene copy number alterations in 242 HER2-positive primary breast cancers. In addition, we examined the correlations between EGFR overexpression, trastuzumab response and clinical outcome in 447 primary, and 112 metastatic HER2-positive breast cancer patients treated by trastuzumab. Of the 242 primary cases, the level of EGFR overexpression was 2+ in 12.7% and 3+ in 11.8%. High EGFR gene copy number was detected in 10.3%. Epidermal growth factor receptor overexpression was associated with hormone receptor negativity and high Ki-67 proliferation index. In survival analyses, EGFR overexpression, but not high EGFR copy number, was associated with poor disease-free survival in all patients, and in the subgroup not receiving adjuvant trastuzumab. In 447 HER2-positive primary breast cancer patients treated with adjuvant trastuzumab, EGFR overexpression was also an independent poor prognostic factor. However, EGFR overexpression was not associated with trastuzumab response, progression-free survival or overall survival in the metastatic setting. Epidermal growth factor receptor overexpression, but not high EGFR copy number, is a poor prognostic factor in HER2-positive primary breast cancer. Epidermal growth factor receptor overexpression is a predictive factor for trastuzumab response in HER2-positive primary breast cancer, but not in metastatic breast cancer.

  3. Copy-Move Forgery Detection Technique for Forensic Analysis in Digital Images

    Directory of Open Access Journals (Sweden)

    Toqeer Mahmood

    2016-01-01

    Full Text Available Due to the powerful image editing tools images are open to several manipulations; therefore, their authenticity is becoming questionable especially when images have influential power, for example, in a court of law, news reports, and insurance claims. Image forensic techniques determine the integrity of images by applying various high-tech mechanisms developed in the literature. In this paper, the images are analyzed for a particular type of forgery where a region of an image is copied and pasted onto the same image to create a duplication or to conceal some existing objects. To detect the copy-move forgery attack, images are first divided into overlapping square blocks and DCT components are adopted as the block representations. Due to the high dimensional nature of the feature space, Gaussian RBF kernel PCA is applied to achieve the reduced dimensional feature vector representation that also improved the efficiency during the feature matching. Extensive experiments are performed to evaluate the proposed method in comparison to state of the art. The experimental results reveal that the proposed technique precisely determines the copy-move forgery even when the images are contaminated with blurring, noise, and compression and can effectively detect multiple copy-move forgeries. Hence, the proposed technique provides a computationally efficient and reliable way of copy-move forgery detection that increases the credibility of images in evidence centered applications.

  4. An aptamer-based biosensor for colorimetric detection of Escherichia coli O157:H7.

    Directory of Open Access Journals (Sweden)

    Wenhe Wu

    Full Text Available BACKGROUND: An aptamer based biosensor (aptasensor was developed and evaluated for rapid colorimetric detection of Escherichia coli (E. coli O157:H7. METHODOLOGY/PRINCIPAL FINDINGS: The aptasensor was assembled by modifying the truncated lipopolysaccharides (LPS-binding aptamer on the surface of nanoscale polydiacetylene (PDA vesicle using peptide bonding between the carboxyl group of the vesicle and the amine group of the aptamer. Molecular recognition between E. coli O157:H7 and aptamer at the interface of the vesicle lead to blue-red transition of PDA which was readily visible to the naked eyes and could be quantified by colorimetric responses (CR. Confocal laser scanning microscope (CLSM and transmission electron microscopy (TEM was used to confirm the specific interactions between the truncated aptamer and E. coli O157:H7. The aptasensor could detect cellular concentrations in a range of 10(4~ 10(8 colony-forming units (CFU/ml within 2 hours and its specificity was 100% for detection of E. coli O157:H7. Compared with the standard culture method, the correspondent rate was 98.5% for the detection of E. coli O157:H7 on 203 clinical fecal specimens with our aptasensor. CONCLUSIONS: The new aptasensor represents a significant advancement in detection capabilities based on the combination of nucleic acid aptamer with PDA vesicle, and offers a specific and convenient screening method for the detection of pathogenic bacteria. This technic could also be applied in areas from clinical analysis to biological terrorism defense, especially in low-resource settings.

  5. A sensitive lateral flow biosensor for Escherichia coli O157:H7 detection based on aptamer mediated strand displacement amplification

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wei [College of Food Science and Engineering, Ocean University of China, Qingdao 266003 (China); Zhao, Shiming [Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530 (China); Mao, Yiping [Yueyang Institute for Food and Drug Control, Yueyang 430198 (China); Fang, Zhiyuan [Affiliated Tumor Hospital of Guangzhou Medical University, Guangzhou 510095 (China); Lu, Xuewen [Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530 (China); Zeng, Lingwen, E-mail: zeng6@yahoo.com [Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530 (China)

    2015-02-25

    Highlights: • Limit of detection as low as 10 CFU mL{sup −1}Escherichia coli O157:H7. • No need of antibodies and substituted with aptamers. • Isothermal strand displacement amplification for signal amplification. • Results observed by the naked eye. • Great potential application in the area of food control. - Abstract: Foodborne diseases caused by pathogens are one of the major problems in food safety. Convenient and sensitive point-of-care rapid diagnostic tests for food-borne pathogens have been a long-felt need of clinicians. Commonly used methods for pathogen detection rely on conventional culture-based tests, antibody-based assays and polymerase chain reaction (PCR)-based techniques. These methods are costly, laborious and time-consuming. Herein, we present a simple and sensitive aptamer based biosensor for rapid detection of Escherichia coli O157:H7 (E. coli O157:H7). In this assay, two different aptamers specific for the outmembrane of E. coli O157:H7 were used. One of the aptamers was used for magnetic bead enrichment, and the other was used as a signal reporter for this pathogen, which was amplified by isothermal strand displacement amplification (SDA) and further detected by a lateral flow biosensor. Only the captured aptamers on cell membrane were amplified, limitations of conventional DNA amplification based method such as false-positive can be largely reduced. The generated signals (red bands on the test zone of a lateral flow strip) can be unambiguously read out by the naked eye. As low as 10 colony forming units (CFU) of E. coli O157:H7 were detected in this study. Without DNA extraction, the reduced handling and simpler equipment requirement render this assay a simple and rapid alternative to conventional methods.

  6. A sensitive lateral flow biosensor for Escherichia coli O157:H7 detection based on aptamer mediated strand displacement amplification

    International Nuclear Information System (INIS)

    Wu, Wei; Zhao, Shiming; Mao, Yiping; Fang, Zhiyuan; Lu, Xuewen; Zeng, Lingwen

    2015-01-01

    Highlights: • Limit of detection as low as 10 CFU mL −1 Escherichia coli O157:H7. • No need of antibodies and substituted with aptamers. • Isothermal strand displacement amplification for signal amplification. • Results observed by the naked eye. • Great potential application in the area of food control. - Abstract: Foodborne diseases caused by pathogens are one of the major problems in food safety. Convenient and sensitive point-of-care rapid diagnostic tests for food-borne pathogens have been a long-felt need of clinicians. Commonly used methods for pathogen detection rely on conventional culture-based tests, antibody-based assays and polymerase chain reaction (PCR)-based techniques. These methods are costly, laborious and time-consuming. Herein, we present a simple and sensitive aptamer based biosensor for rapid detection of Escherichia coli O157:H7 (E. coli O157:H7). In this assay, two different aptamers specific for the outmembrane of E. coli O157:H7 were used. One of the aptamers was used for magnetic bead enrichment, and the other was used as a signal reporter for this pathogen, which was amplified by isothermal strand displacement amplification (SDA) and further detected by a lateral flow biosensor. Only the captured aptamers on cell membrane were amplified, limitations of conventional DNA amplification based method such as false-positive can be largely reduced. The generated signals (red bands on the test zone of a lateral flow strip) can be unambiguously read out by the naked eye. As low as 10 colony forming units (CFU) of E. coli O157:H7 were detected in this study. Without DNA extraction, the reduced handling and simpler equipment requirement render this assay a simple and rapid alternative to conventional methods

  7. Determining Thermal Inactivation of Escherichia coli O157:H7 in Fresh Compost by Simulating Early Phases of the Composting Process ▿

    OpenAIRE

    Singh, Randhir; Kim, Jinkyung; Shepherd, Marion W.; Luo, Feng; Jiang, Xiuping

    2011-01-01

    A three-strain mixture of Escherichia coli O157:H7 was inoculated into fresh dairy compost (ca. 107 CFU/g) with 40 or 50% moisture and was placed in an environmental chamber (ca. 70% humidity) that was programmed to ramp from room temperature to selected composting temperatures in 2 and 5 days to simulate the early composting phase. The surviving E. coli O157:H7 population was analyzed by direct plating and enrichment. Optimal and suboptimal compost mixes, with carbon/nitrogen (C/N) ratios of...

  8. Practical method for appearance match between soft copy and hard copy

    Science.gov (United States)

    Katoh, Naoya

    1994-04-01

    CRT monitors are often used as a soft proofing device for the hard copy image output. However, what the user sees on the monitor does not match its output, even if the monitor and the output device are calibrated with CIE/XYZ or CIE/Lab. This is especially obvious when correlated color temperature (CCT) of CRT monitor's white point significantly differs from ambient light. In a typical office environment, one uses a computer graphic monitor having a CCT of 9300K in a room of white fluorescent light of 4150K CCT. In such a case, human visual system is partially adapted to the CRT monitor's white point and partially to the ambient light. The visual experiments were performed on the effect of the ambient lighting. Practical method for soft copy color reproduction that matches the hard copy image in appearance is presented in this paper. This method is fundamentally based on a simple von Kries' adaptation model and takes into account the human visual system's partial adaptation and contrast matching.

  9. Escherichia coli O157:H7 Outbreak Associated with Restaurant Beef Grinding.

    Science.gov (United States)

    Torso, Lauren M; Voorhees, Ronald E; Forest, Stephen A; Gordon, Andrew Z; Silvestri, Sharon A; Kissler, Bonnie; Schlackman, Jessica; Sandt, Carol H; Toma, Paul; Bachert, Joel; Mertz, Kristen J; Harrison, Lee H

    2015-07-01

    Escherichia coli O157:H7 is a common cause of foodborne illness in the United States. Beef ground at establishments regulated by the U.S. Department of Agriculture, Food Safety and Inspection Service is routinely tested for E. coli O157:H7. Prior to December 2013, boxed beef product (wholesale cuts of beef, such as beef loin, packaged into bags and boxed for shipping) was not always tested for this pathogen. Downstream processors or retailers may grind the product; and, if the ground beef is not cooked to the recommended temperature, pathogens on the exterior of the beef introduced to the interior through grinding may survive. On 18 October 2013, the Allegheny County Health Department identified two E. coli O157:H7 cases, both of whom were food handlers at restaurant A, a restaurant that ground locally produced boxed beef for hamburgers on site. Case finding was conducted through public messaging, employee surveys, and disease surveillance. All potential cases were interviewed using a standard questionnaire. A confirmed case was defined as laboratory-confirmed E. coli O157:H7 with exposure to restaurant A. A probable case was defined as a patient with compatible symptoms and exposure to restaurant A but without laboratory confirmation. All human and food isolates were characterized by pulsed-field gel electrophoresis and multilocus variable-number tandem repeat analysis. The analysis identified 14 confirmed and 10 probable cases of E. coli; 18 nonintact ground beef samples tested positive for E. coli O157:H7. Nine confirmed cases were restaurant A employees. All confirmed cases recalled eating a restaurant A hamburger in the 10 days before illness onset; most cases reported consuming medium to rare hamburgers. Multiple pulsed-field gel electrophoresis and multilocus variable-number tandem repeat analysis patterns were identified among both the human and ground beef isolates, and the patient isolates matched those found in ground beef samples. Restaurant A

  10. Rey-Osterrieth Complex Figure - copy and immediate recall: Normative data for the Latin American Spanish speaking adult population.

    Science.gov (United States)

    Rivera, D; Perrin, P B; Morlett-Paredes, A; Galarza-Del-Angel, J; Martínez, C; Garza, M T; Saracho, C P; Rodríguez, W; Rodríguez-Agudelo, Y; Rábago, B; Aliaga, A; Schebela, S; Luna, M; Longoni, M; Ocampo-Barba, N; Fernández, E; Esenarro, L; García-Egan, P; Arango-Lasprilla, J C

    2015-01-01

    To generate normative data on the Rey-Osterrieth Complex Figure Test (ROCF) across 11 countries in Latin America, with country-specific adjustments for gender, age, and education, where appropriate. The sample consisted of 3,977 healthy adults who were recruited from Argentina, Bolivia, Chile, Cuba, El Salvador, Guatemala, Honduras, Mexico, Paraguay, Peru, and, Puerto Rico. Each subject was administered the ROCF as part of a larger neuropsychological battery. A standardized five-step statistical procedure was used to generate the norms. The final multiple linear regression models explained 7-34% of the variance in ROCF copy scores and 21-41% of the variance in immediate recall scores. Although t-tests showed significant differences between men and women on ROCF copy and immediate recall scores, none of the countries had an effect size larger than 0.3. As a result, gender-adjusted norms were not generated. The present study is the first to create norms for the ROCF in Latin America. As a result, this study will have important implications for the formation and practice of neuropsychology in this region.

  11. Pathogenic Escherichia coli and food handlers in luxury hotels in Nairobi, Kenya.

    Science.gov (United States)

    Onyango, Abel O; Kenya, Eucharia U; Mbithi, John J N; Ng'ayo, Musa O

    2009-11-01

    The epidemiology and virulence properties of pathogenic Escherichia coli among food handlers in tourist destination hotels in Kenya are largely uncharacterized. This cross-sectional study among consenting 885 food handlers working in nine luxurious tourist hotels in Nairobi, Kenya determined the epidemiology, virulence properties, antibiotics susceptibility profiles and conjugation abilities of pathogenic Escherichia coli. Pathogenic Escherichia coli was detected among 39 (4.4%) subjects, including 1.8% enteroaggregative Escherichia coli (EAEC) harboring aggR genes, 1.2% enterotoxigenic Escherichia coli (ETEC) expressing both LT and STp toxins, 1.1% enteropathogenic Escherichia coli (EPEC) and 0.2% Shiga-like Escherichia coli (EHEC) both harboring eaeA and stx2 genes respectively. All the pathotypes had increased surface hydrophobicity. Using multivariate analyses, food handlers with loose stools were more likely to be infected with pathogenic Escherichia coli. Majority 53.8% of the pathotypes were resistant to tetracycline with 40.2% being multi-drug resistant. About 85.7% pathotypes trans-conjugated with Escherichia coli K12 F(-) NA(r) LA. The carriage of multi-drug resistant, toxin expressing pathogenic Escherichia coli by this population is of public health concern because exposure to low doses can result in infection. Screening food handlers and implementing public awareness programs is recommended as an intervention to control transmission of enteric pathogens.

  12. Increased Expression of Cytotoxic T-Lymphocyte-Associated Protein 4 by T Cells, Induced by B7 in Sera, Reduces Adaptive Immunity in Patients With Acute Liver Failure

    DEFF Research Database (Denmark)

    Khamri, Wafa; Abeles, Robin D; Hou, Tie Zheng

    2017-01-01

    , hepatic sinusoidal endothelial cells, and biliary epithelial cells from healthy or diseased liver tissues. We also measured levels of soluble B7 serum samples from patients and controls, and mice with acetaminophen-induced liver injury using enzyme-linked immunosorbent assays. RESULTS: Peripheral blood...... were found to have increased concentrations of soluble B7 compared to sera from controls. Necrotic human primary hepatocytes exposed to acetaminophen, but not hepatic sinusoidal endothelial cells and biliary epithelial cells from patients with ALF, secreted high levels of soluble B7. Sera from mice...... with acetaminophen-induced liver injury contained high levels of soluble B7 compared to sera from mice without liver injury. Plasma exchange reduced circulating levels of soluble B7 in patients with ALF and expression of CTLA4 on T cells. CONCLUSIONS: Peripheral CD4+T cells from patients with ALF have increased...

  13. Occurrence of Coliform and Escherichia coli Contamination and Absence of Escherichia coli O157:H7 on Romaine Lettuce from Retail Stores in the Upper Midwest.

    Science.gov (United States)

    Greve, Josephine D; Zietlow, Mark S; Miller, Kevin M; Ellingson, Jay L E

    2015-09-01

    A total of 720 whole, romaine lettuce heads were purchased from retail locations in the Upper Midwest and assessed for coliform and Escherichia coli contamination and for the presence of E. coli O157:H7. During a 16-month period (August 2010 through December 2011), coliform and E. coli counts were enumerated on Petrifilm, and the presence of E. coli O157:H7 and the virulence gene eae was evaluated by real-time PCR (qPCR). Over half (400 of 720) of the lettuce samples were processed with an immunomagnetic separation step before the qPCR assay. All retail lettuce samples were negative for E. coli O157:H7 when tested with the R.A.P.I.D. LT qPCR targeting a region of the O-antigen, and only two (0.28%) were positive for the eae gene when tested with LightCycler qPCR. On Petrifilm, coliform counts of most lettuce samples (96.4%) were between lettuce samples (98.2%) were lettuce heads. These results contribute to the limited recorded data and understanding of microbial contamination of whole romaine lettuce heads purchased from retail locations, specifically revealing the absence of E. coli O157:H7 and low levels of contamination with coliforms and other E. coli strains.

  14. Proliferation of Escherichia coli O157:H7 in Soil-Substitute and Hydroponic Microgreen Production Systems.

    Science.gov (United States)

    Xiao, Zhenlei; Bauchan, Gary; Nichols-Russell, Lydia; Luo, Yaguang; Wang, Qin; Nou, Xiangwu

    2015-10-01

    Radish (Raphanus sativus var. longipinnatus) microgreens were produced from seeds inoculated with Escherichia coli O157:H7 by using peat moss-based soil-substitute and hydroponic production systems. E. coli populations on the edible and inedible parts of harvested microgreen plants (7 days postseeding) and in growth medium were examined. E. coli O157:H7 was shown to survive and proliferate significantly during microgreen growth in both production systems, with a higher level in the hydroponic production system. At the initial seed inoculation level of 3.7 log CFU/g, E. coli O157:H7 populations on the edible part of microgreen plants reached 2.3 and 2.1 log CFU/g (overhead irrigation and bottom irrigation, respectively) for microgreens from the soil-substitute production system and reached 5.7 log CFU/g for those hydroponically grown. At a higher initial inoculation of 5.6 log CFU/g seeds, the corresponding E. coli O157:H7 populations on the edible parts of microgreens grown in these production systems were 3.4, 3.6, and 5.3 log CFU/g, respectively. Examination of the spatial distribution of bacterial cells on different parts of microgreen plants showed that contaminated seeds led to systematic contamination of whole plants, including both edible and inedible parts, and seed coats remained the focal point of E. coli O157:H7 survival and growth throughout the period of microgreen production.

  15. Comparative analysis of B7-1 and B7-2 expression in Langerhans cells: differential regulation by T helper type 1 and T helper type 2 cytokines.

    Science.gov (United States)

    Kawamura, T; Furue, M

    1995-07-01

    Epidermal Langerhans cells (LC) are Ia-bearing potent antigen-presenting cells (APC) of dendritic cell lineage that play a crucial role in primary and secondary T cell-dependent immune responses. LC express several costimulatory molecules such as B7, which has been implicated as one of the important determinants of professional APC. Recently, B7 antigens have been shown to include three distinct molecules termed B7-1, B7-2, and B7-3, and the expression of B7-1 and B7-2 in LC has been already confirmed. However, little is known of the regulation of B7-1 and B7-2 expression in LC. We demonstrated that LC do not express B7-1 and B7-2 in situ; however, the expression of both molecules is rapidly induced during the first 3 days of culture, and high levels of expression are maintained at least until day 6. We show that the expression of B7-2 in LC is much higher than that of B7-1 in each experiment, and that B7-1 and B7-2 expression is reproducibly augmented by interleukin (IL)-4 in a dose-dependent manner; however, IL-2 affected expression very little. Finally, B7-1 expression is significantly and dose-dependently down-regulated by interferon (IFN)-gamma or IL-10, and B7-2 expression is consistently inhibited by IL-10, but not by IFN-gamma. The effects of these cytokines are active only in the induction phase (during first 3 days of culture) of B7 expression: the modulatory effects of cytokines are hardly detected in the plateau phase (days 4 to 6 of culture) of B7 expression in LC. These findings suggest that B7-1 and B7-2 expression are indeed selectively and differentially regulated by these T cell-derived cytokines, and that the cytokines may modulate the synthesis of B7 molecules rather than the degradation of already-expressed B7 molecules.

  16. Determining the relative contribution and hierarchy of qseBC and hha in the regulation of flagellar motility of Escherichia coli O157:H7

    Science.gov (United States)

    In a recent study we demonstrated that in comparison to the wild-type enterohemorrhagic Escherichia coli (EHEC) O157:H7, a motility-compromised hha deletion mutant with an up-regulated type III secretion system and increased secretion of adherence proteins showed reduced fecal shedding in cattle. In...

  17. Microbial electrolytic disinfection process for highly efficient Escherichia coli inactivation

    DEFF Research Database (Denmark)

    Zhou, Shaofeng; Huang, Shaobin; Li, Xiaohu

    2018-01-01

    extensively studied for recalcitrant organics removal, its application potential towards water disinfection (e.g., inactivation of pathogens) is still unknown. This study investigated the inactivation of Escherichia coli in a microbial electrolysis cell based bio-electro-Fenton system (renamed as microbial......Water quality deterioration caused by a wide variety of recalcitrant organics and pathogenic microorganisms has become a serious concern worldwide. Bio-electro-Fenton systems have been considered as cost-effective and highly efficient water treatment platform technology. While it has been......]OH was identified as one potential mechanism for disinfection. This study successfully demonstrated the feasibility of bio-electro-Fenton process for pathogens inactivation, which offers insight for the future development of sustainable, efficient, and cost-effective biological water treatment technology....

  18. Purification and refolding of anti-T-antigen single chain antibodies (scFvs) expressed in Escherichia coli as inclusion bodies.

    Science.gov (United States)

    Yuasa, Noriyuki; Koyama, Tsubasa; Fujita-Yamaguchi, Yoko

    2014-02-01

    T-antigen (Galβ1-3GalNAcα-1-Ser/Thr) is an oncofetal antigen that is commonly expressed as a carbohydrate determinant in many adenocarcinomas. Since it is associated with tumor progression and metastasis, production of recombinant antibodies specific for T-antigen could lead to the development of cancer diagnostics and therapeutics. Previously, we isolated and characterized 11 anti-T-antigen phage clones from a phage library displaying human single-chain antibodies (scFvs) and purified one scFv protein, 1G11. More recently, we purified and characterized 1E8 scFv protein using a Drosophila S2 expression system. In the current study, four anti-T-antigen scFv genes belonging to Groups 1-4 were purified from inclusion bodies expressed in Escherichia coli cells. Inclusion bodies isolated from E. coli cells were denatured in 3.5 M Gdn-HCl. Solubilized His-tagged scFv proteins were purified using Ni(2+)-Sepharose column chromatography in the presence of 3.5 M Gdn-HCl. Purified scFv proteins were refolded according to a previously published method of step-wise dialysis. Two anti-T-antigen scFv proteins, 1E6 and 1E8 that belong to Groups 1 and 2, respectively, were produced in sufficient amounts, thus allowing further characterization of their binding activity with T-antigen. Specificity and affinity constants determined using enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR), respectively, provided evidence that both 1E8 and 1E6 scFv proteins are T-antigen specific and suggested that 1E8 scFv protein has a higher affinity for T-antigen than 1E6 scFv protein.

  19. Selective Loss of Early Differentiated, Highly Functional PD1high CD4 T Cells with HIV Progression.

    Directory of Open Access Journals (Sweden)

    Robert M Paris

    Full Text Available The role of PD-1 expression on CD4 T cells during HIV infection is not well understood. Here, we describe the differential expression of PD-1 in CD127high CD4 T cells within the early/intermediate differentiated (EI (CD27highCD45RAlow T cell population among uninfected and HIV-infected subjects, with higher expression associated with decreased viral replication (HIV-1 viral load. A significant loss of circulating PD-1highCTLA-4low CD4 T cells was found specifically in the CD127highCD27highCD45RAlow compartment, while initiation of antiretroviral treatment, particularly in subjects with advanced disease, reversed these dynamics. Increased HIV-1 Gag DNA was also found in PD-1high compared to PD-1low ED CD4 T cells. In line with an increased susceptibility to HIV infection, PD-1 expression in this CD4 T cell subset was associated with increased activation and expression of the HIV co-receptor, CCR5. Rather than exhaustion, this population produced more IFN-g, MIP1-a, IL-4, IL-10, and IL-17a compared to PD-1low EI CD4 T cells. In line with our previous findings, PD-1high EI CD4 T cells were also characterized by a high expression of CCR7, CXCR5 and CCR6, a phenotype associated with increased in vitro B cell help. Our data show that expression of PD-1 on early-differentiated CD4 T cells may represent a population that is highly functional, more susceptible to HIV infection and selectively lost in chronic HIV infection.

  20. Shiga toxin-producing Escherichia coli in Central Greece: prevalence and virulence genes of O157:H7 and non-O157 in animal feces, vegetables, and humans.

    Science.gov (United States)

    Pinaka, O; Pournaras, S; Mouchtouri, V; Plakokefalos, E; Katsiaflaka, A; Kolokythopoulou, F; Barboutsi, E; Bitsolas, N; Hadjichristodoulou, C

    2013-11-01

    In Greece, Shiga toxin-producing Escherichia coli (STEC) have only been sporadically reported. The objective of this study was to estimate the prevalence of STEC and Escherichia coli O157:H7 in farm animals, vegetables, and humans in Greece. A total number of 1,010 fecal samples were collected from farm animals (sheep, goats, cattle, chickens, pigs), 667 diarrheal samples from humans, and 60 from vegetables, which were cultured in specific media for STEC isolates. Enzyme-linked immunosorbent assay (ELISA) was used to detect toxin-producing colonies, which, subsequently, were subjected to a multiplex polymerase chain reaction (PCR) for stx1, stx2, eae, rfbE O157, and fliC h7 genes. Eighty isolates (7.9 %) from animal samples were found to produce Shiga toxin by ELISA, while by PCR, O157 STEC isolates were detected from 8 (0.8 %) samples and non-O157 STEC isolates from 43 (4.2 %) samples. STEC isolates were recovered mainly from sheep and goats, rarely from cattle, and not from pigs and chickens, suggesting that small ruminants constitute a potential risk for human infections. However, only three human specimens (0.4 %) were positive for the detection of Shiga toxins and all were PCR-negative. Similarly, all 60 vegetable samples were negative for toxin production and for toxin genes, but three samples (two roman rockets and one spinach) were positive by PCR for rfbE O157 and fliC h7 genes. These findings indicate that sheep, goats, cattle, and leafy vegetables can be a reservoir of STEC and Escherichia coli O157:H7 isolates in Greece, which are still rarely detected among humans.

  1. Characterization of the Copy Number and Variants of Deformed Wing Virus (DWV in the Pairs of Honey Bee Pupa and Infesting Varroa destructor or Tropilaelaps mercedesae

    Directory of Open Access Journals (Sweden)

    Yunfei Wu

    2017-08-01

    Full Text Available Recent honey bee colony losses, particularly during the winter, have been shown to be associated with the presence of both ectoparasitic mites and Deformed Wing Virus (DWV. Whilst the role of Varroa destructor mites as a viral vector is well established, the role of Tropilaelaps mercedesae mites in viral transmission has not been fully investigated. In this study, we tested the effects that V. destructor and T. mercedesae infestation have on fluctuation of the DWV copy number and alteration of the virus variants in honey bees by characterizing individual pupae and their infesting mites. We observed that both mite species were associated with increased viral copy number in honey bee pupae. We found a positive correlation between DWV copy number in pupae and copy number in infesting mites, and the same DWV type A variant was present in either low or high copy number in both honey bee pupae and infesting V. destructor. These data also suggest that variant diversity is similar between honey bee pupae and the mites that infest them. These results support a previously proposed hypothesis that DWV suppresses the honey bee immune system when virus copy number reaches a specific threshold, promoting greater replication.

  2. ANTIMICIROBIAL SUSCEPTIBILITY PATTERNS OF Escherichia coli ...

    African Journals Online (AJOL)

    DR. AMINU

    A total of 56 and 24 strains of E. coli and Shigella sp. isolated from children less than five years with diarrhoea attending 3 ... parasitic infections, as well as food intolerance, reaction to ..... Escherichia coil 0157:H7 as a model of entry of a new.

  3. Microbiota response to Escherichia coli O157:H7 colonization in cattle

    Science.gov (United States)

    Cattle are primary reservoir of Shiga toxin-producing Escherichia coli (STEC). Field studies indicate STEC colonization influences gut microbiota composition in beef and dairy cattle. In this pilot study, we evaluated the bovine gut microbiota after STEC O157 (O157) challenge under experimental con...

  4. Atmospheric cold plasma inactivation of Escherichia coli 0157:H7 and aerobic microorganisms in cold-stored romaine lettuce packaged in a commerical polyethylene terephthalate container

    Science.gov (United States)

    Leafy greens continue to be a significant vector for foodborne pathogens, including Escherichia coli O157:H7. Dielectric barrier discharge atmospheric cold plasma (ACP) treatment is a promising method for microbial decontamination of produce. An important aspect of this technology is the potential f...

  5. Advanced MR methods at ultra-high field (7 Tesla) for clinical musculoskeletal applications

    Energy Technology Data Exchange (ETDEWEB)

    Trattnig, Siegfried [Medical University of Vienna/Vienna General Hospital, MR Centre - High Field MR, Department of Radiology, Vienna (Austria); Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Austrian Cluster for Tissue Regeneration, Vienna (Austria); Zbyn, Stefan; Schmitt, Benjamin; Friedrich, Klaus; Bogner, Wolfgang [Medical University of Vienna/Vienna General Hospital, MR Centre - High Field MR, Department of Radiology, Vienna (Austria); Juras, Vladimir; Szomolanyi, Pavol [Medical University of Vienna/Vienna General Hospital, MR Centre - High Field MR, Department of Radiology, Vienna (Austria); Slovak Academy of Sciences, Department of Imaging Methods, Institute of Measurement Science, Bratislava (Slovakia)

    2012-11-15

    This article provides an overview of the initial clinical results of musculoskeletal studies performed at 7 Tesla, with special focus on sodium imaging, new techniques such as chemical exchange saturation transfer (CEST) and T2* imaging, and multinuclear MR spectroscopy. Sodium imaging was clinically used at 7 T in the evaluation of patients after cartilage repair procedures because it enables the GAG content to be monitored over time. Sodium imaging and T2* mapping allow insights into the ultra-structural composition of the Achilles tendon and help detect early disease. Chemical exchange saturation transfer was, for the first time, successfully applied in the clinical set-up at 7 T in patients after cartilage repair surgery. The potential of phosphorus MR spectroscopy in muscle was demonstrated in a comparison study between 3 and 7 T, with higher spectral resolution and significantly shorter data acquisition times at 7 T. These initial clinical studies demonstrate the potential of ultra-high field MR at 7 T, with the advantage of significantly improved sensitivity for other nuclei, such as {sup 23}Na (sodium) and {sup 31}P (phosphorus). The application of non-proton imaging and spectroscopy provides new insights into normal and abnormal physiology of musculoskeletal tissues, particularly cartilage, tendons, and muscles. (orig.)

  6. Effect of storage temperaturas on growth and survival of Escherichia coli 0157: H7 inoculated in foods from a neotropical environment

    Directory of Open Access Journals (Sweden)

    María Laura Arias

    2001-06-01

    Full Text Available Escherichia coli 0157: H7 has emerged as a new pathogen and is found worldwide. We studied the effect of several storage temperatures on the survival of this bacterium in common foods from a neotropical environment (Costa Rica because at least seven clinical cases have been reported from the country, and no epidemiological link or probable food association has been described. High (106- 108 CFU/ml and low (104-106 CFU/ml populations of E. coli were inoculated (three replications in ground meat, chopped cabbage, chicken giblets and pasteurized milk and incubated at 0, 6 and 12 °C for 24, 48 and 72 h. Vegetables and milk were also stored at 22 °C for the sarne periods.The E. coli 0157: H7 enumeration was done according to the methodology describes in the Bacteriological Analytical Manual. Populations of E. coli 0157: H7 showed either an increasing or decreasing trend, according to temperature, time or food base. Our data indicate that E. coli 0157: H7 is capable of surviving and growing in meat, cabbage, milk and chicken giblets; food items commonly consunied by Costa Ricans.Escherichia coli 0157, H7 ha emergido como un nuevo patógeno y se encuentra mundialmente. En Costa Rica, por lo menos ha informado de siete casos clínicos, y no se ha encontrado un lazo epidemiológico o asociación con alimentos. El propósito de este estudio fue determinar el efecto de diferentes temperaturas de almacenamiento sobre la sobrevivencia de esta bacteria en alimentos de uso común. Una población alta de E. Coli (106- 108 UFC/ml y una baja (104-106 UFC/ml fueron inoculadas (tres réplicas en carne picada, repollo picado, vísceras de pollo y leche pasteurizada e incubadas a 0, 6 y 1 °C por 24, 48 y 72 h. Los vegetales y la leche también fueron incubados a 22 °C por los mismos períodos. La enumeración de E. Coli 0157: H7 se realizó de acuerdo a la metodología descrita en el Bacteriological Analytical Manual. Las poblaciones de E. coli mostraron

  7. High Spatial Resolution Cardiovascular Magnetic Resonance at 7.0 Tesla in Patients with Hypertrophic Cardiomyopathy – First Experiences: Lesson Learned from 7.0 Tesla

    Science.gov (United States)

    Prothmann, Marcel; von Knobelsdorff-Brenkenhoff, Florian; Töpper, Agnieszka; Dieringer, Matthias A.; Shahid, Etham; Graessl, Andreas; Rieger, Jan; Lysiak, Darius; Thalhammer, C.; Huelnhagen, Till; Kellman, Peter; Niendorf, Thoralf; Schulz-Menger, Jeanette

    2016-01-01

    Background Cardiovascular Magnetic Resonance (CMR) provides valuable information in patients with hypertrophic cardiomyopathy (HCM) based on myocardial tissue differentiation and the detection of small morphological details. CMR at 7.0T improves spatial resolution versus today’s clinical protocols. This capability is as yet untapped in HCM patients. We aimed to examine the feasibility of CMR at 7.0T in HCM patients and to demonstrate its capability for the visualization of subtle morphological details. Methods We screened 131 patients with HCM. 13 patients (9 males, 56 ±31 years) and 13 healthy age- and gender-matched subjects (9 males, 55 ±31years) underwent CMR at 7.0T and 3.0T (Siemens, Erlangen, Germany). For the assessment of cardiac function and morphology, 2D CINE imaging was performed (voxel size at 7.0T: (1.4x1.4x2.5) mm3 and (1.4x1.4x4.0) mm3; at 3.0T: (1.8x1.8x6.0) mm3). Late gadolinium enhancement (LGE) was performed at 3.0T for detection of fibrosis. Results All scans were successful and evaluable. At 3.0T, quantification of the left ventricle (LV) showed similar results in short axis view vs. the biplane approach (LVEDV, LVESV, LVMASS, LVEF) (p = 0.286; p = 0.534; p = 0.155; p = 0.131). The LV-parameters obtained at 7.0T where in accordance with the 3.0T data (pLVEDV = 0.110; pLVESV = 0.091; pLVMASS = 0.131; pLVEF = 0.182). LGE was detectable in 12/13 (92%) of the HCM patients. High spatial resolution CINE imaging at 7.0T revealed hyperintense regions, identifying myocardial crypts in 7/13 (54%) of the HCM patients. All crypts were located in the LGE-positive regions. The crypts were not detectable at 3.0T using a clinical protocol. Conclusions CMR at 7.0T is feasible in patients with HCM. High spatial resolution gradient echo 2D CINE imaging at 7.0T allowed the detection of subtle morphological details in regions of extended hypertrophy and LGE. PMID:26863618

  8. Dose-Dependent Effects of Lactobacillus rhamnosus on Serum Interleukin-17 Production and Intestinal T-Cell Responses in Pigs Challenged with Escherichia coli

    Science.gov (United States)

    Zhu, Yao-Hong; Li, Xiao-Qiong; Zhang, Wei; Zhou, Dong; Liu, Hao-Yu

    2014-01-01

    The mechanism underlying the dose effect of probiotics on ameliorating diarrhea has not been fully elucidated. Here, low (1 × 109 CFU/ml) or high (1 × 1011 CFU/ml) doses of Lactobacillus rhamnosus ATCC 7469 were administered orally to piglets for 1 week before F4 (K88)-positive enterotoxigenic Escherichia coli (F4+ ETEC) challenge. Administration of a low, but not a high, dose of L. rhamnosus decreased the percentage of CD3+ CD4+ CD8− T cells in the peripheral blood. Notably, transiently increased serum concentrations of interleukin-17A (IL-17A) were observed after F4+ ETEC challenge in pigs pretreated with a high dose of L. rhamnosus. Administration of L. rhamnosus increased the percentage of the small intestinal lamina propria CD3+ CD4+ CD8− cells and Peyer's patch CD3+ CD4− CD8− and CD3− CD4− CD8+ cells. The percentage of ileal intraepithelial CD3+ CD4− CD8+ cells increased only in the high-dose piglets. Administration of L. rhamnosus downregulated expression of ileal IL-17A after F4+ ETEC challenge but had no effect on expression of gamma interferon (IFN-γ), IL-12, IL-4, and FOXP3 mRNA in the small intestine. Expression of jejunal IL-2, ileal transforming growth factor β1 (TGF-β1), and ileal IL-10 was upregulated in the low-dose piglets after F4+ ETEC challenge. Our findings suggest that amelioration of infectious diarrhea in piglets by L. rhamnosus is associated with the generation of lamina propria CD3+ CD4+ CD8− T cells, the expansion of Peyer's patch CD3+ CD4− CD8− and CD3− CD4− CD8+ cells, and the attenuation of F4+ ETEC-induced increase in CD3+ CD4+ CD8+ T cells in the small intestine. However, consumption of high doses of L. rhamnosus may increase levels of serum IL-17A after F4+ ETEC challenge, thus eliciting a strong proinflammatory response. PMID:24389928

  9. HER-2 immunohistochemical expression as prognostic marker in high-grade T1 bladder cancer (T1G3

    Directory of Open Access Journals (Sweden)

    Luca Bongiovanni

    2013-06-01

    Full Text Available Objectives: To evaluate if the Human epidermal growth factor receptor 2 (HER-2 expression levels may be used as potential prognostic marker in high grade T1 blad- der cancer (T1G3 Methods: Specimens from transurethral resection of bladder tumour (TURBT of 103 patients with high-grade T1 bladder cancer were collected. This pathologic database was reviewed. Four-year follow-up data were matched with pathologic data. Eighty-three patients entered the study. HER-2 staining was performed. Patients were grouped for HER-2 status. Statistical analysis included Kaplan Meier survival analysis and Log-rank test. Results: Pathological review of TURBT specimens confirmed high-grade T1 transitional cell bladder cancer in all patients. Median follow-up was 12 months (mean 23,5; range 3-48. Twenty-one patients (25.4% present strong HER-2 expression (3+, 28 (33.7% moderate expression (2+, 26 (33.7% weak staining (1+ and 8 (9.6% negative expression (0. Thirty- one patients of 83 (37.4% had not evidence of disease, 41 (49.4% recurred, 11 (13.2% had a progression of disease. Forty-one patients had high grade T1 recurrence. Patients with HER-2 status 0 did not showed progression of disease. Patients with HER-2 status 3+, undergoing cys- tectomy because progression of disease, had a pathological stage > pT2 and a nodal involve- ment. Median Disease-Free Survival (DFS for all patients was 12 months (DFS probability (pDFS = 49.3%; 95% CI, -11.1/+10.1. Median DFS in HER-2 groups was 8 (pDFS 37.5%; 95% CI,-28.8/+29.9, 24 (pDFS 46.1%; 95% CI,-19.5/+17.5, 20 (pDFS 46.4%; 95% CI,-18.8/+16.9 and 10 months (pDFS 47.6%; 95% CI,-21.9/+19.1 respectively in HER-2 status 0,1+,2+,3+. Log-Rank test is not statistically significant (p = 0,39. Conclusions: This study showed that HER-2 expression does not represent a prognostic mark- er of recurrence/progression of disease in high-grade T1 bladder cancer.

  10. Bovine Colostral Antibody Against Verotoxin 2 Derived from Escherichia coli O157:H7: Resistance to Proteases and Effects in Beagle Dogs

    Science.gov (United States)

    Kuribayashi, Takashi; Seita, Tetsuro; Matsumoto, Mariko; Furuhata, Katsunori; Tagata, Kazutoshi; Yamamoto, Shizuo

    2009-01-01

    A bovine colostral antibody against verotoxin (VT) 2 of Escherichia coli O157:H7 was administered orally to beagle dogs. The antibody remained in the dogs’ small intestine for at least 2 h, whereas little serum antibody remained 1.5 h after administration. Furthermore, the antibody activity of secretory IgA did not change until 2 h after administration; however, the activity of IgG and IgM antibodies decreased by approximately 60% and 40% at 2 h after administration, respectively. Seven beagle dogs inoculated with Escherichia coli O157:H7 producing VT2 were administered bovine colostral antibody or bovine colostral whey without antibody. With administration of bovine colostral whey without antibody, the amount of VT2 in feces decreased gradually after administration and increased again at 5 d after inoculation, whereas bovine colostral antibody significantly reduced the amount of VT2 in feces on the day after administration. In addition, 9 beagle dogs were given bovine colostral antibody, bovine plasma antibody, or saline. The amount of VT2 in feces again decreased significantly more rapidly after administration of bovine colostral antibody than after administration of bovine plasma antibody or saline. PMID:19389308

  11. Cooperative Actions of CRP-cAMP and FNR Increase the Fosfomycin Susceptibility of Enterohaemorrhagic Escherichia coli (EHEC) by Elevating the Expression of glpT and uhpT under Anaerobic Conditions.

    Science.gov (United States)

    Kurabayashi, Kumiko; Tanimoto, Koichi; Tomita, Haruyoshi; Hirakawa, Hidetada

    2017-01-01

    Bacterial infections to anaerobic site are often hard to be treated because the activity of most of antimicrobials decreases under anaerobic conditions. However, fosfomycin rather provides a greater activity under anaerobic conditions than aerobic conditions. Previously, we found that expression of glpT and uhpT , fosfomycin symporters in enterohaemorrhagic Escherichia coli (EHEC) was upregulated by FNR, a global regulator during the anaerobiosis of the bacterium, which led to increased uptake and susceptibility to this drug. In this study, we showed that expression of glpT and uhpT is induced by CRP-cAMP, the regulator complex under both aerobic and anaerobic conditions. The activity of CRP-cAMP in EHEC was elevated under anaerobic conditions because levels of both CRP and cAMP were higher in the cells when grown anaerobically than those when grown aerobically. Results of expression study using mutants indicated that CRP-cAMP is indispensable for expression of glpT but not uhpT -whereas that of uhpT requires UhpA that is the response regulator composing of two-component system with the sensor kinase, UhpB. The CRP-cAMP protein bound to a region that overlaps RNA polymerase binding site for glpT and region upstream of UhpA binding site for uhpT . FNR bound to a region further upstream of CRP-cAMP binding site on region upstream of the glpT gene. These combined results suggested that increased antibacterial activity of fosfomycin to EHEC under anaerobic conditions is due to activation of FNR and increment of CRP-cAMP activity. Then, FNR enhances the expression of glpT activated by CRP-cAMP while CRP-cAMP and FNR cooperatively aids the action of UhpA to express uhpT to maximum level.

  12. The antimicrobial peptide cathelicidin protects mice from Escherichia coli O157:H7-mediated disease.

    Directory of Open Access Journals (Sweden)

    Milan Chromek

    Full Text Available This study investigated the role of the antimicrobial peptide cathelicidin in Escherichia coli O157:H7 infection and subsequent renal damage. Mouse and human cathelicidin, CRAMP and LL-37, respectively, killed E. coli O157:H7 in vitro. Intestines from healthy wild-type (129/SvJ and cathelicidin-knock-out (Camp(-/- mice were investigated, showing that cathelicidin-deficient mice had a thinner colonic mucus layer compared with wild-type mice. Wild-type (n = 11 and cathelicidin-knock-out (n = 11 mice were inoculated with E. coli O157:H7. Cathelicidin-deficient animals exhibited higher fecal counts of E. coli O157:H7 and bacteria penetrated the mucus forming attaching-and-effacing lesions to a much higher extent than in wild-type animals. Cathelicidin knock-out mice developed symptoms (9/11 as well as anemia, thrombocytopenia and extensive renal tubular damage while all cathelicidin-producing mice remained asymptomatic with normal laboratory findings. When injected with Shiga toxin intraperitoneally, both murine strains developed the same degree of renal tubular damage and clinical disease indicating that differences in sensitivity to infection between the murine strains were related to the initial intestinal response. In conclusion, cathelicidin substantially influenced the antimicrobial barrier in the mouse colon mucosa. Cathelicidin deficiency lead to increased susceptibility to E. coli O157:H7 infection and subsequent renal damage. Administration of cathelicidin or stimulation of endogenous production may prove to be novel treatments for E. coli O157:H7-induced hemolytic uremic syndrome.

  13. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies.

    Science.gov (United States)

    Roller, Benjamin R K; Stoddard, Steven F; Schmidt, Thomas M

    2016-09-12

    The potential for rapid reproduction is a hallmark of microbial life, but microbes in nature must also survive and compete when growth is constrained by resource availability. Successful reproduction requires different strategies when resources are scarce and when they are abundant 1,2 , but a systematic framework for predicting these reproductive strategies in bacteria has not been available. Here, we show that the number of ribosomal RNA operons (rrn) in bacterial genomes predicts two important components of reproduction-growth rate and growth efficiency-which are favoured under contrasting regimes of resource availability 3,4 . We find that the maximum reproductive rate of bacteria doubles with a doubling of rrn copy number, and the efficiency of carbon use is inversely related to maximal growth rate and rrn copy number. We also identify a feasible explanation for these patterns: the rate and yield of protein synthesis mirror the overall pattern in maximum growth rate and growth efficiency. Furthermore, comparative analysis of genomes from 1,167 bacterial species reveals that rrn copy number predicts traits associated with resource availability, including chemotaxis and genome streamlining. Genome-wide patterns of orthologous gene content covary with rrn copy number, suggesting convergent evolution in response to resource availability. Our findings imply that basic cellular processes adapt in contrasting ways to long-term differences in resource availability. They also establish a basis for predicting changes in bacterial community composition in response to resource perturbations using rrn copy number measurements 5 or inferences 6,7 .

  14. 7 T body MRI: B1 shimming with simultaneous SAR reduction

    International Nuclear Information System (INIS)

    Bergen, Bob van den; Berg, Cornelis A T van den; Bartels, Lambertus W; Lagendijk, Jan J W

    2007-01-01

    The high frequency of the radiofrequency (RF) fields used in high field magnetic resonance imaging (MRI) results in electromagnetic field variations that can cause local regions to have a large specific absorption rate (SAR) and/or a low excitation. In this study, we evaluated the use of a B 1 shimming technique which can simultaneously improve the B + 1 homogeneity and reduce the SAR for whole body imaging at 7 T. Optimizations for four individual anatomies showed a reduction up to 74% of the peak SAR values with respect to a quadrature excitation and a simultaneous improvement of the B + 1 homogeneity varying between 39 and 75% for different optimization parameters. The average SAR was reduced with approximately 50% for all optimizations. The optimized phase and amplitude settings from an elliptical phantom model were applied to four realistic human anatomy models to evaluate whether a generic application without prior knowledge of the detailed human anatomy is possible. This resulted in an average improvement of the B + 1 homogeneity of 37% and an average reduction of the maximum and average SAR of 50 and 55%, respectively. It can be concluded that this generic method can be used as a simple method to improve the prospects of 7 T body imaging

  15. Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli

    Directory of Open Access Journals (Sweden)

    Katie H. Jameson

    2017-01-01

    Full Text Available Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication. In contrast, cells entering the sporulation pathway in B. subtilis can do so only during a short interval in the cell cycle when there are two, and only two, chromosomes per cell, one destined for the spore and one for the mother cell. Here, we briefly describe the overall process of DNA replication in bacteria before reviewing initiation of DNA replication in detail. The review covers DnaA-directed assembly of the replisome at oriC and the multitude of mechanisms of regulation of initiation, with a focus on the similarities and differences between E. coli and B. subtilis.

  16. Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli

    Science.gov (United States)

    Jameson, Katie H.; Wilkinson, Anthony J.

    2017-01-01

    Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication. In contrast, cells entering the sporulation pathway in B. subtilis can do so only during a short interval in the cell cycle when there are two, and only two, chromosomes per cell, one destined for the spore and one for the mother cell. Here, we briefly describe the overall process of DNA replication in bacteria before reviewing initiation of DNA replication in detail. The review covers DnaA-directed assembly of the replisome at oriC and the multitude of mechanisms of regulation of initiation, with a focus on the similarities and differences between E. coli and B. subtilis. PMID:28075389

  17. Deteksi Pemalsuan Citra dengan Teknik Copy-Move Menggunakan Metode Ordinal Measure dari Koefisien Discrete Cosine Transform

    Directory of Open Access Journals (Sweden)

    Zulfan

    2016-07-01

    Full Text Available This article discusses a new method for the detection of forgery images generated by copy-move technique. Copy-move technique is one of image forgery techniques which taking a particular object from its original image and add it on that image for the purpose of increasing the number of or changing the same object in the original image. This study aims to detect the forged image generated by the copy-move techniques and copy-move forged image that has been modified by the rotation operation and histogram equalization. Detection feature used is Ordinal Measure of Discrete Cosine Transform coefficient (OM-DCT. Detection starts with division of the image into a block size of BXB (B = 16x16, 32x32 and 64x64 and two-dimensional DCT was performed to each of blocks. The feature distance from the original to the fake image, was calculated by the Euclidian distance and each feature has a distance of less than or equal to the threshold value (T according to the observations will be marked as a forged part. The results show that there are blocks detected on the copy-move image, whether on the unmodified copy-move forge image or those which modified by the rotation operation and histogram equalization. The number of blocks that are found in the copy-move object varies according to the size of the detection block used.

  18. Prevalence of Escherichia Coli O157:H7 and Enterobacteriaceae on Hands of Workers in Halal Cattle Abattoirs in Peninsular Malaysia

    Science.gov (United States)

    Shamsul, Bahri Mohd Tamrin; Adamu, Muhammad Tukur; Mohd Desa, Mohd Nasir; Khairani-Bejo, Siti

    2016-01-01

    Background Several occupational diseases of multiple origins are encountered among abattoir workers. Presence of indicator microorganisms (coliforms) on hands of workers can be used a gauge for hygienic practices. Methods A cross-sectional study was performed to assess the prevalence of E.coli and enterobacteriaceae among Halal abattoir workers in some government halal abattoirs of Malaysia. A total of one hundred and sixty-five hand swab samples were collected from workers of Halal abattoirs in Malaysia. The samples were subjected to microbiological analysis for characterisation and serotyping. Results The results have shown that no Escherichia coli O157:H7 was isolated on the hands of abattoir workers before and after work. However, a total prevalence of 9.7% was recorded for all samples during work. For non-O157:H7, total prevalence of 33.3% during work and 13% after work were obtained. High prevalence was recorded in sample taken during work from Tampin, Jasin and Kemaman (100% each) while low prevalence where observed in Shah Alam, Banting and Ipoh (20% each). Conclusions Based on the findings the hygienic practices of hand washing among the workers in few locations was found to be low especially after work. PMID:27904427

  19. Assessment of cartilage-dedicated sequences at ultra-high-field MRI: comparison of imaging performance and diagnostic confidence between 3.0 and 7.0 T with respect to osteoarthritis-induced changes at the knee joint

    Energy Technology Data Exchange (ETDEWEB)

    Stahl, Robert [University of California, Musculoskeletal and Quantitative Imaging Group, Department of Radiology, San Francisco, CA (United States); University Hospitals - Campus Grosshadern, Ludwig Maximilians University of Munich, Department of Clinical Radiology, Munich (Germany); Krug, Roland; Zuo, Jin; Majumdar, Sharmila; Link, Thomas M. [University of California, Musculoskeletal and Quantitative Imaging Group, Department of Radiology, San Francisco, CA (United States); Kelley, Douglas A.C. [General Electrics Healthcare Technologies, San Francisco, CA (United States); Ma, C.B. [University of California, Department of Orthopedic Surgery, San Francisco, CA (United States)

    2009-08-15

    The objectives of the study were to optimize three cartilage-dedicated sequences for in vivo knee imaging at 7.0 T ultra-high-field (UHF) magnetic resonance imaging (MRI) and to compare imaging performance and diagnostic confidence concerning osteoarthritis (OA)-induced changes at 7.0 and 3.0 T MRI. Optimized MRI sequences for cartilage imaging at 3.0 T were tailored for 7.0 T: an intermediate-weighted fast spin-echo (IM-w FSE), a fast imaging employing steady-state acquisition (FIESTA) and a T1-weighted 3D high-spatial-resolution volumetric fat-suppressed spoiled gradient-echo (SPGR) sequence. Three healthy subjects and seven patients with mild OA were examined. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diagnostic confidence in assessing cartilage abnormalities, and image quality were determined. Abnormalities were assessed with the whole organ magnetic resonance imaging score (WORMS). Focal cartilage lesions and bone marrow edema pattern (BMEP) were also quantified. At 7.0 T, SNR was increased (p<0.05) for all sequences. For the IM-w FSE sequence, limitations with the specific absorption rate (SAR) required modifications of the scan parameters yielding an incomplete coverage of the knee joint, extensive artifacts, and a less effective fat saturation. CNR and image quality were increased (p<0.05) for SPGR and FIESTA and decreased for IM-w FSE. Diagnostic confidence for cartilage lesions was highest (p<0.05) for FIESTA at 7.0 T. Evaluation of BMEP was decreased (p < 0.05) at 7.0 T due to limited performance of IM-w FSE. Gradient echo-based pulse sequences like SPGR and FIESTA are well suited for imaging at UHF which may improve early detection of cartilage lesions. However, UHF IM-w FSE sequences are less feasible for clinical use. (orig.)

  20. Assessment of cartilage-dedicated sequences at ultra-high-field MRI: comparison of imaging performance and diagnostic confidence between 3.0 and 7.0 T with respect to osteoarthritis-induced changes at the knee joint

    International Nuclear Information System (INIS)

    Stahl, Robert; Krug, Roland; Zuo, Jin; Majumdar, Sharmila; Link, Thomas M.; Kelley, Douglas A.C.; Ma, C.B.

    2009-01-01

    The objectives of the study were to optimize three cartilage-dedicated sequences for in vivo knee imaging at 7.0 T ultra-high-field (UHF) magnetic resonance imaging (MRI) and to compare imaging performance and diagnostic confidence concerning osteoarthritis (OA)-induced changes at 7.0 and 3.0 T MRI. Optimized MRI sequences for cartilage imaging at 3.0 T were tailored for 7.0 T: an intermediate-weighted fast spin-echo (IM-w FSE), a fast imaging employing steady-state acquisition (FIESTA) and a T1-weighted 3D high-spatial-resolution volumetric fat-suppressed spoiled gradient-echo (SPGR) sequence. Three healthy subjects and seven patients with mild OA were examined. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diagnostic confidence in assessing cartilage abnormalities, and image quality were determined. Abnormalities were assessed with the whole organ magnetic resonance imaging score (WORMS). Focal cartilage lesions and bone marrow edema pattern (BMEP) were also quantified. At 7.0 T, SNR was increased (p<0.05) for all sequences. For the IM-w FSE sequence, limitations with the specific absorption rate (SAR) required modifications of the scan parameters yielding an incomplete coverage of the knee joint, extensive artifacts, and a less effective fat saturation. CNR and image quality were increased (p<0.05) for SPGR and FIESTA and decreased for IM-w FSE. Diagnostic confidence for cartilage lesions was highest (p<0.05) for FIESTA at 7.0 T. Evaluation of BMEP was decreased (p < 0.05) at 7.0 T due to limited performance of IM-w FSE. Gradient echo-based pulse sequences like SPGR and FIESTA are well suited for imaging at UHF which may improve early detection of cartilage lesions. However, UHF IM-w FSE sequences are less feasible for clinical use. (orig.)

  1. R7T7 nuclear waste glass behavior in moist clay: role of the clay mass/glass surface area ratio

    International Nuclear Information System (INIS)

    Godon, N.; Vernaz, E.

    1989-01-01

    R7T7 glass alteration was investigated in the presence of various moist clays. In contact with smectite 4a, selected in France as a potential engineered barrier material, the glass was significantly corroded: after 6 months the glass corrosion rate was practically the same as the initial alteration rate in double-distilled water. Substantially lower alteration was observed in contact with bentonite 6 activated by sodium carbonate. Smectite 4a consumes silicon released by glass corrosion, and thus retards the rise to high silicon concentrations in solution at which the glass corrosion rate diminishes. Glass can therefore in some cases be altered as much in moist clay as in water with high renewal rates. Other experiments with smaller quantities of smectite 4a showed that the phenomenon becomes less important in time: its duration is proportional to the ratio between the clay mass (C) and the glass surface area (SA). Comparing the results of studies at different C/SA ratios indicates that low glass corrosion rates are obtained more slowly at higher C/SA ratios. Tests with 239 Pu-doped R7T7 glass also showed that the radionuclide retention factor in the alteration film at the glass surface is only 6, compared with a factor of nearly 50 in double-distilled water

  2. Imaging the intracranial atherosclerotic vessel wall using 7T MRI: initial comparison with histopathology

    NARCIS (Netherlands)

    van der Kolk, A. G.; Zwanenburg, J. J. M.; Denswil, N. P.; Vink, A.; Spliet, W. G. M.; Daemen, M. J. A. P.; Visser, F.; Klomp, D. W. J.; Luijten, P. R.; Hendrikse, J.

    2015-01-01

    Several studies have attempted to characterize intracranial atherosclerotic plaques by using MR imaging sequences. However, dedicated validation of these sequences with histology has not yet been performed. The current study assessed the ability of ultra-high-resolution 7T MR imaging sequences with

  3. Spiral MR fingerprinting at 7T with simultaneous B1 estimation.

    Science.gov (United States)

    Buonincontri, Guido; Schulte, Rolf F; Cosottini, Mirco; Tosetti, Michela

    2017-09-01

    Magnetic resonance fingerprinting is an efficient, new approach for quantitative imaging with MR. We aimed to extend this technique to cases with B1+ inhomogeneities within the imaging volume. Previous approaches have used abrupt changes in flip angles to estimate the B1+ field simultaneously with T1 and T2, using a Cartesian approach in a small-animal scanner at 4.7T. Here, we evaluated whether a similar approach would be suitable for imaging human brains using spiral readouts with a 7T scanner. We found that our modified scheme could significantly reduce the adverse effects of B1+ inhomogeneities even in extreme cases, reducing both the bias and the variance in T2 estimations by an order of magnitude when compared to literature methods. Acquisitions used less than 1.5W/kg SAR and could be performed in 12s per slice. In conclusion, our approach can be used to perform quantitative imaging of the brain at 7T in a short time, simultaneously estimating the B1+ profile. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. 36 CFR 1290.6 - Originals and copies.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Originals and copies. 1290.6... ASSASSINATION RECORDS COLLECTION ACT OF 1992 (JFK ACT) § 1290.6 Originals and copies. (a) For purposes of determining whether originals or copies of assassination records will be made part of the President John F...

  5. Preservation Copying Endangered Historic Negative Collections

    DEFF Research Database (Denmark)

    Kejser, Ulla Bøgvad

    2008-01-01

    This article discusses preservation copying of unstable B&W nitrate and acetate still photographic negatives. It focuses on evaluating two different strategies for preserving the copies from a point of view of quality and cost-effectiveness. The evaluated strategies are preservation of the master...... by describing essential characteristics of negatives, which must be passed on to the copies, and the required metadata and technical imaging specifications. Next the paper discusses strategies for preservation and makes an analysis with the LIFE2 Costing Model. The paper concludes that the most beneficial...... and cost-effective preservation solution for large format negatives is to keep the preservation copies as digital files. However, it also acknowledges that it is important to revisit such strategies regularly to monitor changes in user expectations, technologies and costs....

  6. Effects of MgO on short and long term stabilities in water of R7T7 and M7 nuclear waste glasses

    Energy Technology Data Exchange (ETDEWEB)

    Advocat, T; Vernaz, E; Dussossoy, J [CEA Centre d` Etudes de la Vallee du Rhone, 30 - Marcoule (France). Dept. des Procedes de Retraitement; Crovisier, J L [Centre National de la Recherche Scientifique (CNRS), 67 - Strasbourg (France)

    1993-12-31

    Magnesium oxide was added to the standard R7T7 and M7 glass compositions developed for containment of fission product solutions. M7 differs from the R7T7 reference glass mainly by a larger proportion of network modifier elements and a correspondingly lower proportion of glass network forming elements. The percentage of fission products, simulated in this study by inactive elements, was the same in both cases. Increasing the MgO content of the glass compositions by 2 to 5 wt% resulted in significant variations in the aqueous leaching resistance at 90 and 100 deg C. Experimental findings demonstrated that the initial dissolution rate measured at 100 deg C in a Soxhlet apparatus was proportional to the MgO content and inversely proportional to the network former content (mainly SiO2). This was confirmed by a glass hydration model based on the thermodynamic stability of the glass matrix components. Aqueous corrosion tests were also conducted at 90 deg C under static conditions at various SA/V ratios to simulate the progress of the reaction. Under these conditions, the glass dissolution rate diminished more slowly in time when the initial magnesium content was high and the network former content was low. This may be due primarily to a variation in the glass silica solubility limit related to the glass composition; it may also be related to the formation of secondary silica and magnesia alteration products controlling the glass dissolution reaction affinity.

  7. COPI is required for enterovirus 71 replication.

    Directory of Open Access Journals (Sweden)

    Jianmin Wang

    Full Text Available Enterovirus 71 (EV71, a member of the Picornaviridae family, is found in Asian countries where it causes a wide range of human diseases. No effective therapy is available for the treatment of these infections. Picornaviruses undergo RNA replication in association with membranes of infected cells. COPI and COPII have been shown to be involved in the formation of picornavirus-induced vesicles. Replication of several picornaviruses, including poliovirus and Echovirus 11 (EV11, is dependent on COPI or COPII. Here, we report that COPI, but not COPII, is required for EV71 replication. Replication of EV71 was inhibited by brefeldin A and golgicide A, inhibitors of COPI activity. Furthermore, we found EV71 2C protein interacted with COPI subunits by co-immunoprecipitation and GST pull-down assay, indicating that COPI coatomer might be directed to the viral replication complex through viral 2C protein. Additionally, because the pathway is conserved among different species of enteroviruses, it may represent a novel target for antiviral therapies.

  8. Copy-Editing: The Cambridge Handbook.

    Science.gov (United States)

    Butcher, Judith

    This handbook is designed as a reference manual for copy editors who prepare typescript for printing. It deals with the following topics: the copy editor's function; the work to be done at each stage in the production process; some difficult points of spelling, capitalization, and other features collectively known as "house style"; the parts of a…

  9. Comparison of 7.0- and 3.0-T MRI and MRA in ischemic-type moyamoya disease: preliminary experience.

    Science.gov (United States)

    Deng, Xiaofeng; Zhang, Zihao; Zhang, Yan; Zhang, Dong; Wang, Rong; Ye, Xun; Xu, Long; Wang, Bo; Wang, Kai; Zhao, Jizong

    2016-06-01

    OBJECT The authors compared the image quality and diagnostic sensitivity and specificity of 7.0-T and 3.0-T MRI and time-of-flight (TOF) MR angiography (MRA) in patients with moyamoya disease (MMD). METHODS MR images of 15 patients with ischemic-type MMD (8 males, 7 females; age 13-48 years) and 13 healthy controls (7 males, 6 females; age 19-28 years) who underwent both 7.0-T and 3.0-T MRI and MRA were studied retrospectively. The main intracranial arteries were assessed by using the modified Houkin's grading system (MRA score). Moyamoya vessels (MMVs) were evaluated by 2 grading systems: the MMV quality score and the MMV area score. Two diagnostic criteria for MMD were used: the T2 criteria, which used flow voids in the basal ganglion on T2-weighted images, and the TOF criteria, which used the high-intensity areas in the basal ganglion on source images from TOF MRA. All data were evaluated by 2 independent readers who were blinded to the strength field and presence or absence of MMD. Using conventional angiography as the gold standard, the sensitivity and specificity of 7.0-T and 3.0-T MRI/MRA in the diagnosis of MMD were calculated. The differences between 7.0-T and 3.0-T MRI and MRA were statistically compared. RESULTS No significant differences were observed between 7.0-T and 3.0-T MRA in MRA score (p = 0.317) or MRA grade (p = 0.317). There was a strong correlation between the Suzuki's stage and MRA grade in both 3.0-T (rs = 0.930; p 3.0-T MRA, suggested by both the MMV quality score (p = 0.001) and the MMV area score (p = 0.001). The correlation between the Suzuki's stage and the MMV area score was moderate in 3.0-T MRA (rs = 0.738; p = 0.002) and strong in 7.0-T MRA (rs = 0.908; p 3.0-T MRI/MRA (sensitivity 0.692; specificity 0.933) in diagnosing MMD; based on the TOF criteria, 7.0-T MRI/MRA was more sensitive (1.000 vs 0.733, respectively) and more specific (1.000 vs 0.923, respectively) than 3.0-T MRI/MRA. CONCLUSIONS Compared with 3.0-T MRI/MRA, 7.0-T

  10. High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

    Science.gov (United States)

    Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

    2012-01-01

    Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

  11. A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

    Science.gov (United States)

    Bloom-Ackermann, Zohar; Navon, Sivan; Gingold, Hila; Towers, Ruth; Pilpel, Yitzhak; Dahan, Orna

    2014-01-01

    Deciphering the architecture of the tRNA pool is a prime challenge in translation research, as tRNAs govern the efficiency and accuracy of the process. Towards this challenge, we created a systematic tRNA deletion library in Saccharomyces cerevisiae, aimed at dissecting the specific contribution of each tRNA gene to the tRNA pool and to the cell's fitness. By harnessing this resource, we observed that the majority of tRNA deletions show no appreciable phenotype in rich medium, yet under more challenging conditions, additional phenotypes were observed. Robustness to tRNA gene deletion was often facilitated through extensive backup compensation within and between tRNA families. Interestingly, we found that within tRNA families, genes carrying identical anti-codons can contribute differently to the cellular fitness, suggesting the importance of the genomic surrounding to tRNA expression. Characterization of the transcriptome response to deletions of tRNA genes exposed two disparate patterns: in single-copy families, deletions elicited a stress response; in deletions of genes from multi-copy families, expression of the translation machinery increased. Our results uncover the complex architecture of the tRNA pool and pave the way towards complete understanding of their role in cell physiology. PMID:24453985

  12. Investigation of Copy Number Variation in Children with Conotruncal Heart Defects

    International Nuclear Information System (INIS)

    Campos, Carla Marques Rondon; Zanardo, Evelin Aline; Dutra, Roberta Lelis; Kulikowski, Leslie Domenici; Kim, Chong Ae

    2015-01-01

    Congenital heart defects (CHD) are the most prevalent group of structural abnormalities at birth and one of the main causes of infant morbidity and mortality. Studies have shown a contribution of the copy number variation in the genesis of cardiac malformations. Investigate gene copy number variation (CNV) in children with conotruncal heart defect. Multiplex ligation-dependent probe amplification (MLPA) was performed in 39 patients with conotruncal heart defect. Clinical and laboratory assessments were conducted in all patients. The parents of the probands who presented abnormal findings were also investigated. Gene copy number variation was detected in 7/39 patients: 22q11.2 deletion, 22q11.2 duplication, 15q11.2 duplication, 20p12.2 duplication, 19p deletion, 15q and 8p23.2 duplication with 10p12.31 duplication. The clinical characteristics were consistent with those reported in the literature associated with the encountered microdeletion/microduplication. None of these changes was inherited from the parents. Our results demonstrate that the technique of MLPA is useful in the investigation of microdeletions and microduplications in conotruncal congenital heart defects. Early diagnosis of the copy number variation in patients with congenital heart defect assists in the prevention of morbidity and decreased mortality in these patients

  13. Investigation of Copy Number Variation in Children with Conotruncal Heart Defects

    Energy Technology Data Exchange (ETDEWEB)

    Campos, Carla Marques Rondon, E-mail: carlamcampos@uol.com.br [Universidade Federal de Mato Grosso, Cuiabá, MT (Brazil); Zanardo, Evelin Aline; Dutra, Roberta Lelis [Departamento de Patologia - Laboratório de Citogenômica - LIM 03 - Universidade de São Paulo, São Paulo, SP (Brazil); Kulikowski, Leslie Domenici [Universidade de São Paulo, São Paulo, SP (Brazil); Departamento de Patologia - Laboratório de Citogenômica - LIM 03 - Universidade de São Paulo, São Paulo, SP (Brazil); Kim, Chong Ae [Universidade de São Paulo, São Paulo, SP (Brazil)

    2015-01-15

    Congenital heart defects (CHD) are the most prevalent group of structural abnormalities at birth and one of the main causes of infant morbidity and mortality. Studies have shown a contribution of the copy number variation in the genesis of cardiac malformations. Investigate gene copy number variation (CNV) in children with conotruncal heart defect. Multiplex ligation-dependent probe amplification (MLPA) was performed in 39 patients with conotruncal heart defect. Clinical and laboratory assessments were conducted in all patients. The parents of the probands who presented abnormal findings were also investigated. Gene copy number variation was detected in 7/39 patients: 22q11.2 deletion, 22q11.2 duplication, 15q11.2 duplication, 20p12.2 duplication, 19p deletion, 15q and 8p23.2 duplication with 10p12.31 duplication. The clinical characteristics were consistent with those reported in the literature associated with the encountered microdeletion/microduplication. None of these changes was inherited from the parents. Our results demonstrate that the technique of MLPA is useful in the investigation of microdeletions and microduplications in conotruncal congenital heart defects. Early diagnosis of the copy number variation in patients with congenital heart defect assists in the prevention of morbidity and decreased mortality in these patients.

  14. Modified Vero cell induced by Bifidobacterium bifidum inhibits enterohemorrhagic Escherichia coli O157:H7 cytopathic effect

    Directory of Open Access Journals (Sweden)

    Tahamtan, Y.

    2014-11-01

    Full Text Available Enterohemorrhagic Escherichia coli (EHEC, such as E. coli O157:H7, are emerging food-borne pathogens worldwide. This micro-organism can damage the epithelial tissue of the large intestine. The cytotoxic effects can be neutralized by probiotics such as Bifidobacterium bifidum. Probiotics are viable cells that have beneficial effects on the health of the host. The preventing activity of B. bifidum against E. coli O157 was studied using a Vero cell model. Vero cell was pretreated with viable B. bifidum and incubated for either 3 h to 24 h and then collected from the cell to make modified Vero cell (MVC. Indirect antibacterial effects of B. bifidum were demonstrated by reduction of attachment of E. coli O157:H7 to MVC. The maximum reduction was resulted in pretreatment of Vero cell with B. bifidum for 24 h before infection. B. bifidum attenuated E. coli O157:H7 attachment to MVC up to 10 days of incubation. To our knowledge, MCV prevented Vero cell line injury induced by E. coli O157:H7. Therefore, B. bifidum can be used for inhibition of E. coli O157:H7 cytopathic effect (CPE in Vero cell model, even as pretreatment of the cell line.

  15. Superconducting 7 T Wave Length Shifter for BESSY-II

    CERN Document Server

    Borovikov, V M; Fedurin, M G; Repkov, V V; Karpov, G V; Kulipanov, G N; Kuzin, M V; Mezentsev, N A; Shkaruba, V A; Krämer, Dietrich; Richter, D

    2001-01-01

    A superconducting 3-pole Wave Length Shifter (WLS) with a maximum field of 7 T was fabricated and tested by BINP in collaboration with BESSY-II. The radiation point is fixed in the center of WLS at any field level by using two correctors. The magnetic field is stabilized with an accuracy of 10 sup - sup 4 at 7 T by a feedback system based on NMR probes and magnetic flux pumps. Persistent current operation mode is enabled by using superconducting persistent keys. The magnetic field homogeneity of 10 sup - sup 4 at 7 T is obtained as a result of shimming in the aperture of the magnet. A protection system based on cold diodes and dump resistors prevents the destruction of superconducting coils during the quench. Two screens with temperatures of 20 and 60 K cooled by cooling machine, two recondensers, HTSC current leads and cevlar suspensions of helium volume are used to decrease liquid helium consumption. The main features and operating mode of the WLS are described.

  16. Interleukin-7 induces HIV replication in primary naive T cells through a nuclear factor of activated T cell (NFAT)-dependent pathway

    International Nuclear Information System (INIS)

    Managlia, Elizabeth Z.; Landay, Alan; Al-Harthi, Lena

    2006-01-01

    Interleukin (IL)-7 plays several roles critical to T cell maturation, survival, and homeostasis. Because of these functions, IL-7 is under investigation as an immune-modulator for therapeutic use in lymphopenic clinical conditions, including HIV. We reported that naive T cells, typically not permissive to HIV, can be productively infected when pre-treated with IL-7. We evaluated the mechanism by which IL-7-mediates this effect. IL-7 potently up-regulated the transcriptional factor NFAT, but had no effect on NFκB. Blocking NFAT activity using a number of reagents, such as Cyclosporin A, FK-506, or the NFAT-specific inhibitor known as VIVIT peptide, all markedly reduced IL-7-mediated induction of HIV replication in naive T cells. Additional neutralization of cytokines present in IL-7-treated cultures and/or those that have NFAT-binding sequences within their promotors indicated that IL-10, IL-4, and most significantly IFNγ, all contribute to IL-7-induction of HIV productive replication in naive T cells. These data clarify the mechanism by which IL-7 can overcome the block to HIV productive infection in naive T cells, despite their quiescent cell status. These findings are relevant to the treatment of HIV disease and understanding HIV pathogenesis in the naive CD4+ T cell compartment, especially in light of the vigorous pursuit of IL-7 as an in vivo immune modulator

  17. Single-copy insertion of transgenes in Caenorhabditis elegans

    DEFF Research Database (Denmark)

    Frøkjaer-Jensen, Christian; Davis, M Wayne; Hopkins, Christopher E

    2008-01-01

    developed a method that inserts a single copy of a transgene into a defined site. Mobilization of a Mos1 transposon generates a double-strand break in noncoding DNA. The break is repaired by copying DNA from an extrachromosomal template into the chromosomal site. Homozygous single-copy insertions can...... be obtained in less than 2 weeks by injecting approximately 20 worms. We have successfully inserted transgenes as long as 9 kb and verified that single copies are inserted at the targeted site. Single-copy transgenes are expressed at endogenous levels and can be expressed in the female and male germlines....

  18. High fusion performance at high T i/T e in JET-ILW baseline plasmas with high NBI heating power and low gas puffing

    Science.gov (United States)

    Kim, Hyun-Tae; Sips, A. C. C.; Romanelli, M.; Challis, C. D.; Rimini, F.; Garzotti, L.; Lerche, E.; Buchanan, J.; Yuan, X.; Kaye, S.; contributors, JET

    2018-03-01

    This paper presents the transport analysis of high density baseline discharges in the 2016 experimental campaign of the Joint European Torus with the ITER-Like Wall (JET-ILW), where a significant increase in the deuterium-deuterium (D-D) fusion neutron rate (~2.8  ×  1016 s-1) was achieved with stable high neutral beam injection (NBI) powers of up to 28 MW and low gas puffing. Increase in T i exceeding T e were produced for the first time in baseline discharges despite the high electron density; this enabled a significant increase in the thermal fusion reaction rate. As a result, the new achieved record in fusion performance was much higher than the previous record in the same heating power baseline discharges, where T i  =  T e. In addition to the decreases in collisionality and the increases in ion heating fraction in the discharges with high NBI power, T i  >  T e can also be attributed to positive feedback between the high T i/T e ratio and stabilisation of the turbulent heat flux resulting from the ion temperature gradient driven mode. The high T i/T e ratio was correlated with high rotation frequency. Among the discharges with identical beam heating power, higher rotation frequencies were observed when particle fuelling was provided by low gas puffing and pellet injection. This reveals that particle fuelling played a key role for achieving high T i/T e, and the improved fusion performance.

  19. Increased Expression of Cytotoxic T-Lymphocyte-Associated Protein 4 by T Cells, Induced by B7 in Sera, Reduces Adaptive Immunity in Patients With Acute Liver Failure

    DEFF Research Database (Denmark)

    Khamri, Wafa; Abeles, Robin D; Hou, Tie Zheng

    2017-01-01

    , hepatic sinusoidal endothelial cells, and biliary epithelial cells from healthy or diseased liver tissues. We also measured levels of soluble B7 serum samples from patients and controls, and mice with acetaminophen-induced liver injury using enzyme-linked immunosorbent assays. RESULTS: Peripheral blood...... mice with acetaminophen-induced liver injury contained high levels of soluble B7 compared to sera from mice without liver injury. Plasma exchange reduced circulating levels of soluble B7 in patients with ALF and expression of CTLA4 on T cells. CONCLUSIONS: Peripheral CD4+ T cells from patients with ALF......BACKGROUND & AIMS: Patients with acute liver failure (ALF) have defects in innate immune responses to microbes (immune paresis) and are susceptible to sepsis. Cytotoxic T-lymphocyte-associated protein 4 (CTLA4), which interacts with the membrane receptor B7 (also called CD80 and CD86...

  20. Salt at concentrations relevant to meat processing enhances Shiga toxin 2 production in Escherichia coli O157:H7.

    Science.gov (United States)

    Harris, Shaun M; Yue, Wan-Fu; Olsen, Sarena A; Hu, Jia; Means, Warrie J; McCormick, Richard J; Du, Min; Zhu, Mei-Jun

    2012-10-15

    Escherichia coli (E. coli) O157:H7 remains a major food safety concern associated with meat, especially beef products. Shiga toxins (Stx) are key virulence factors produced by E. coli O157:H7 that are responsible for hemorrhagic colitis and Hemolytic Uremic Syndrome. Stx are heat stable and can be absorbed after oral ingestion. Despite the extensive study of E. coli O157:H7 survival during meat processing, little attention is paid to the production of Stx during meat processing. The objective of this study was to elucidate the effect of salt, an essential additive to processed meat, at concentrations relevant to meat processing (0%, 1%, 2%, 3%, W/V) on Stx2 production and Stx2 prophage induction by E. coli O157:H7 strains. For both E. coli O157:H7 86-24 and EDL933 strains, including 2% salt in LB broth decreased (Pmeat processing enhances Stx production, a process linked to bacterial stress response and lambdoid prophage induction. Published by Elsevier B.V.