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Journal articles on the topic 'Genomic DNA of E.coli analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Vilen, Heikki, Juha-Matti Aalto, Anna Kassinen, Lars Paulin, and Harri Savilahti. "A Direct Transposon Insertion Tool for Modification and Functional Analysis of Viral Genomes." Journal of Virology 77, no. 1 (2003): 123–34. http://dx.doi.org/10.1128/jvi.77.1.123-134.2003.

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ABSTRACT Advances in DNA transposition technology have recently generated efficient tools for various types of functional genetic analyses. We demonstrate here the power of the bacteriophage Mu-derived in vitro DNA transposition system for modification and functional characterization of a complete bacterial virus genome. The linear double-stranded DNA genome of Escherichia coli bacteriophage PRD1 was studied by insertion mutagenesis with reporter mini-Mu transposons that were integrated in vitro into isolated genomic DNA. After introduction into bacterial cells by electroporation, recombinant

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2

Dobrindt, Ulrich, Franziska Agerer, Kai Michaelis, et al. "Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays." Journal of Bacteriology 185, no. 6 (2003): 1831–40. http://dx.doi.org/10.1128/jb.185.6.1831-1840.2003.

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ABSTRACT Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied.

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3

Kang, Yujin, Jinyong Lee, Jisoo Kim, et al. "Analysis of alcohol-induced DNA damage in Escherichia coli by visualizing single genomic DNA molecules." Analyst 141, no. 14 (2016): 4326–31. http://dx.doi.org/10.1039/c6an00616g.

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4

Baumler, David J., Lois M. Banta, Kai F. Hung, et al. "Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis." CBE—Life Sciences Education 11, no. 1 (2012): 81–93. http://dx.doi.org/10.1187/cbe.10-04-0057.

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Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virule

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CAO, YINHE, WEN-WEN TUNG, J. B. GAO, and YAN QI. "RECURRENCE TIME STATISTICS: VERSATILE TOOLS FOR GENOMIC DNA SEQUENCE ANALYSIS." Journal of Bioinformatics and Computational Biology 03, no. 03 (2005): 677–96. http://dx.doi.org/10.1142/s0219720005001235.

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With the completion of the human and a few model organisms' genomes, and with the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time-based me

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6

Herbelin, Corinne J., Samantha C. Chirillo, Kristen A. Melnick, and Thomas S. Whittam. "Gene Conservation and Loss in themutS-rpoS Genomic Region of PathogenicEscherichia coli." Journal of Bacteriology 182, no. 19 (2000): 5381–90. http://dx.doi.org/10.1128/jb.182.19.5381-5390.2000.

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ABSTRACT The extent and nature of DNA polymorphism in themutS-rpoS region of the Escherichia coli genome were assessed in 21 strains of enteropathogenic E. coli(EPEC) and enterohemorrhagic E. coli (EHEC) and in 6 strains originally isolated from natural populations. The intervening region between mutS and rpoS was amplified by long-range PCR, and the resulting amplicons varied substantially in length (7.8 to 14.2 kb) among pathogenic groups. Restriction maps based on five enzymes and sequence analysis showed that strains of the EPEC 1, EPEC 2, and EHEC 2 groups have a long mutS-rpoS region com

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7

Grozdanov, Lubomir, Carsten Raasch, Jürgen Schulze, et al. "Analysis of the Genome Structure of the Nonpathogenic Probiotic Escherichia coli Strain Nissle 1917." Journal of Bacteriology 186, no. 16 (2004): 5432–41. http://dx.doi.org/10.1128/jb.186.16.5432-5441.2004.

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ABSTRACT Nonpathogenic Escherichia coli strain Nissle 1917 (O6:K5:H1) is used as a probiotic agent in medicine, mainly for the treatment of various gastroenterological diseases. To gain insight on the genetic level into its properties of colonization and commensalism, this strain's genome structure has been analyzed by three approaches: (i) sequence context screening of tRNA genes as a potential indication of chromosomal integration of horizontally acquired DNA, (ii) sequence analysis of 280 kb of genomic islands (GEIs) coding for important fitness factors, and (iii) comparison of Nissle 1917

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8

Parekh, Virali J., Frank Wien, Wilfried Grange, Thomas A. De Long, Véronique Arluison, and Richard R. Sinden. "Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability." Microorganisms 8, no. 10 (2020): 1598. http://dx.doi.org/10.3390/microorganisms8101598.

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G-rich DNA repeats that can form G-quadruplex structures are prevalent in bacterial genomes and are frequently associated with regulatory regions of genes involved in virulence, antigenic variation, and antibiotic resistance. These sequences are also inherently mutagenic and can lead to changes affecting cell survival and adaptation. Transcription of the G-quadruplex-forming repeat (G3T)n in E. coli, when mRNA comprised the G-rich strand, promotes G-quadruplex formation in DNA and increases rates of deletion of G-quadruplex-forming sequences. The genomic instability of G-quadruplex repeats may

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9

Willenbrock, Hanni, Anne Petersen, Camilla Sekse, Kristoffer Kiil, Yngvild Wasteson, and David W. Ussery. "Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling." Journal of Bacteriology 188, no. 22 (2006): 7713–21. http://dx.doi.org/10.1128/jb.01043-06.

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ABSTRACT We describe the design and evaluate the use of a high-density oligonucleotide microarray covering seven sequenced Escherichia coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands, and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 (Δstx 2::cat) as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labeled genomic DNA to query the microarrays and subsequently analyze common virulence genes and phage elements

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10

Gomez-Duarte, Oscar, Julio Guerra, and Ricky Ko. "1127. Genomic Analysis of Biofilm-Forming Enteroinvasive E. coli Emergent Pathogen." Open Forum Infectious Diseases 5, suppl_1 (2018): S337—S338. http://dx.doi.org/10.1093/ofid/ofy210.960.

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Abstract Background Enteroinvasive Escherichia coli (EIEC) are involved in dysenteric diarrhea among children in low- and middle-income countries. EIEC strains isolated in Colombia, South America were shown to form biofilms and to be invasive in vitro. The O96:H19 serotypes and biofilm formation (BF) are not common phenotypes among EIEC, and the role they may play in diarrhea is at present unknown. The main goal of this study was to identify virulence and BF genes from EIEC genomic data. We hypothesize that EIEC O96:H19 strain 52.1 originated from horizontal transfer of a Shigella-like virulen

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Venieri, D., A. Vantarakis, G. Komninou, and M. Papapetropoulou. "Differentiation of faecal Escherichia coli from human and animal sources by random amplified polymorphic DNA-PCR (RAPD-PCR)." Water Science and Technology 50, no. 1 (2004): 193–98. http://dx.doi.org/10.2166/wst.2004.0053.

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In this study the assessment of randomly amplified polymorphic DNA (RAPD) analysis was established as a molecular epidemiological tool. RAPD analysis was performed to differentiate faecal Escherichia coli isolates from human and animal sources. E. coli strains (128) were isolated from human and animal faeces (from cattle and sheep). Genomic DNA was extracted and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting was performed. Seven arbitrary primers were tested with a view to discriminating between E. coli isolates from humans and E. coli isolates from animals. RAPD profiles wer

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12

Han, Min-Ah, Heung-Shick Lee, Choong-Ill Cheon, Kyung-Hee Min, and Myeong-Sok Lee. "Cloning and analysis of the aroB gene encoding dehydroquinate synthase from Corynebacterium glutamicum." Canadian Journal of Microbiology 45, no. 10 (1999): 885–90. http://dx.doi.org/10.1139/w99-076.

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The aroB gene encoding dehydroquinate synthase of Corynebacterium glutamicum has been cloned by complementation of an aro auxotrophic mutant of Escherichia coli with the genomic DNA library. The recombinant plasmid contained a 1.4-kb fragment that complemented the Escherichia coli dehydroquinate-synthase-deficient mutant. The nucleotide sequences of the subcloned DNA has been determined. The sequences contain an open reading frame of 360 codons, from which a protein with a molecular mass of about 38 kDa could be predicted. This is consistent with the size of the AroB protein expressed in E. co

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13

Brahami, Anissa, Annie Castonguay, and Éric Déziel. "Novel ‘Bacteriospray’ Method Facilitates the Functional Screening of Metagenomic Libraries for Antimicrobial Activity." Methods and Protocols 2, no. 1 (2019): 4. http://dx.doi.org/10.3390/mps2010004.

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Metagenomic techniques, notably the cloning of environmental DNA (eDNA) into surrogate hosts, have given access to the genome of uncultured bacteria. However, the determination of gene functions based on DNA sequences alone remains a significant challenge. The functional screening of metagenomic libraries represents an interesting approach in the discovery of microbial metabolites. We describe here an optimized screening approach that facilitates the identification of new antimicrobials among large metagenomic libraries. Notably, we report a detailed genomic library construction protocol using

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14

Marri, Laura, Emanuela Barboni, Tiziana Irdani, Brunella Perito, and Giorgio Mastromei. "Restriction enzyme and DNA hybridization analysis of cellulolytic Streptomyces isolates of different origin." Canadian Journal of Microbiology 43, no. 4 (1997): 395–99. http://dx.doi.org/10.1139/m97-055.

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Streptomyces rochei A2 endoglucanase (eglS) and β-glucosidase (bgs1) genes were used as probes to survey their distribution among 16 Streptomyces strains isolated from different sources and characterized for their cellulolytic activities. The eglS probe hybridized to the genomic DNA of 12 strains with a restriction pattern different from that of S. rochei A2. The DNA from all strains, except one, hybridized with the bgsl probe and one strain showed the same restriction pattern as seen in S. rochei A2. The sequence localized by the eglS probe in S. thermoviolaceus and the one localized by the b

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15

B., Mullaney P., Marks D. J., and Pallavicini G. M. "Mimotopes and Proteome Analyses Using Human Genomic andcDNA Epitope Phage Display." Comparative and Functional Genomics 3, no. 3 (2002): 254–63. http://dx.doi.org/10.1002/cfg.174.

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In the post-genomic era, validation of candidate gene targets frequently requires proteinbased strategies. Phage display is a powerful tool to define protein-protein interactions by generating peptide binders against target antigens. Epitope phage display libraries have the potential to enrich coding exon sequences from human genomic loci. We evaluated genomic and cDNA phage display strategies to identify genes in the 5q31 Interleukin gene cluster and to enrich cell surface receptor tyrosine kinase genes from a breast cancer cDNA library. A genomic display library containing 2 ×106clones with

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16

Matic, I., M. Radman, and C. Rayssiguier. "Structure of recombinants from conjugational crosses between Escherichia coli donor and mismatch-repair deficient Salmonella typhimurium recipients." Genetics 136, no. 1 (1994): 17–26. http://dx.doi.org/10.1093/genetics/136.1.17.

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Abstract To get more insight into the control of homologous recombination between diverged DNA by the Mut proteins of the long-patch mismatch repair system, we have studied interspecies Escherichia coli/Salmonella typhimurium recombination. Knowing that the same recombination pathway (RecABCD) is responsible for intraspecies and interspecies recombination, we have now studied the structure (replacement vs. addition-type or other rearrangement-type recombinants) of 81 interspecies recombinants obtained in conjugational crosses between E. coli donor and mutL, mutS, mutH, mutU or mut+ S. typhimur

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17

Pradel, Nathalie, Sabine Leroy-Setrin, Bernard Joly, and Valérie Livrelli. "Genomic Subtraction To Identify and Characterize Sequences of Shiga Toxin-Producing Escherichia coli O91:H21." Applied and Environmental Microbiology 68, no. 5 (2002): 2316–25. http://dx.doi.org/10.1128/aem.68.5.2316-2325.2002.

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ABSTRACT To identify Shiga toxin-producing Escherichia coli genes associated with severe human disease, a genomic subtraction technique was used with hemolytic-uremic syndrome-associated O91:H21 strain CH014 and O6:H10 bovine strains. The method was adapted to the Shiga toxin-producing E. coli genome: three rounds of subtraction were used to isolate DNA fragments specific to strain CH014. The fragments were characterized by genetic support analysis, sequencing, and hybridization to the genome of a collection of Shiga toxin-producing E. coli strains. A total of 42 fragments were found, 19 of wh

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18

Schneider-Scherzer, E., B. Auer, E. J. de Groot, and M. Schweiger. "Primary structure of a DNA (N6-adenine)-methyltransferase from Escherichia coli virus T1. DNA sequence, genomic organization, and comparative analysis." Journal of Biological Chemistry 265, no. 11 (1990): 6086–91. http://dx.doi.org/10.1016/s0021-9258(19)39295-6.

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19

Grainger, David C., Timothy W. Overton, Nikos Reppas, et al. "Genomic Studies with Escherichia coli MelR Protein: Applications of Chromatin Immunoprecipitation and Microarrays." Journal of Bacteriology 186, no. 20 (2004): 6938–43. http://dx.doi.org/10.1128/jb.186.20.6938-6943.2004.

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ABSTRACT Escherichia coli MelR protein is a transcription activator that is essential for melibiose-dependent expression of the melAB genes. We have used chromatin immunoprecipitation to study the binding of MelR and RNA polymerase to the melAB promoter in vivo. Our results show that MelR is associated with promoter DNA, both in the absence and presence of the inducer melibiose. In contrast, RNA polymerase is recruited to the melAB promoter only in the presence of inducer. The MelR DK261 positive control mutant binds to the melAB promoter but cannot recruit RNA polymerase. Further analysis of

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Thiaville, Jennifer J., Stefanie M. Kellner, Yifeng Yuan, et al. "Novel genomic island modifies DNA with 7-deazaguanine derivatives." Proceedings of the National Academy of Sciences 113, no. 11 (2016): E1452—E1459. http://dx.doi.org/10.1073/pnas.1518570113.

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The discovery of ∼20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant

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Prilipov, Alexej, Prashant S. Phale, Ralf Koebnik, Christine Widmer, and Jurg P. Rosenbusch. "Identification and Characterization of Two Quiescent Porin Genes, nmpC and ompN, inEscherichia coli BE." Journal of Bacteriology 180, no. 13 (1998): 3388–92. http://dx.doi.org/10.1128/jb.180.13.3388-3392.1998.

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ABSTRACT The genomic DNA of the BE strain of Escherichia coli has been scrutinized to detect porin genes that have not been identified so far. Southern blot analysis yielded two DNA segments which proved highly homologous to, yet distinct from, theompC, ompF, and phoE porin genes. The two genes were cloned and sequenced. One of them, designatedompN, encodes a porin which, due to low levels of expression, has eluded prior identification. The functional properties (single-channel conductance) of the OmpN porin, purified to homogeneity, closely resemble those of the OmpC porin fromE. coli K-12. T

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Munson, George P., Lisa G. Holcomb, Heather L. Alexander, and June R. Scott. "In Vitro Identification of Rns-Regulated Genes." Journal of Bacteriology 184, no. 4 (2002): 1196–99. http://dx.doi.org/10.1128/jb.184.4.1196-1199.2002.

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ABSTRACT To identify Rns-regulated genes, a maltose binding protein (MBP)-Rns fusion protein was used to isolate DNA fragments from enterotoxigenic Escherichia coli genomic DNA that carry Rns binding sites. In vivo transcription fusion analysis shows that Rns positively regulates the expression of the open reading frame of yiiS, which lies immediately downstream of one MBP-Rns-bound fragment.

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23

Li, Dongmei, Jie Cheng, Ziang Zhu, et al. "Treg‐inducing capacity of genomic DNA of Bifidobacterium longum subsp. infantis." Allergy and Asthma Proceedings 41, no. 5 (2020): 372–85. http://dx.doi.org/10.2500/aap.2020.41.200064.

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Background: Allergic and autoimmune diseases comprise a group of inflammatory disorders caused by aberrant immune responses in which CD25+ forkhead box P3‐positive regulatory T cells (Treg) cells that normally suppress inflammatory events are often poorly functioning. This has stimulated an intensive investigative effort to find ways of increasing Tregs as a method of therapy for these conditions. Commensal microbiota known to have health benefits in humans include the lactic acid‐producing, probiotic bacteria B. longum subsp. infantis and Lactobacillus rhamnosus. Mechanistically, several mech

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Osorio, Carlos R., Joeli Marrero, Rachel A. F. Wozniak, Manuel L. Lemos, Vincent Burrus, and Matthew K. Waldor. "Genomic and Functional Analysis of ICEPdaSpa1, a Fish-Pathogen-Derived SXT-Related Integrating Conjugative Element That Can Mobilize a Virulence Plasmid." Journal of Bacteriology 190, no. 9 (2008): 3353–61. http://dx.doi.org/10.1128/jb.00109-08.

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ABSTRACT Integrating conjugative elements (ICEs) are self-transmissible mobile elements that transfer between bacteria via conjugation and integrate into the host chromosome. SXT and related ICEs became prevalent in Asian Vibrio cholerae populations in the 1990s and play an important role in the dissemination of antibiotic resistance genes in V. cholerae. Here, we carried out genomic and functional analyses of ICEPdaSpa1, an SXT-related ICE derived from a Spanish isolate of Photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis. The ∼102-kb DNA sequence of ICEPdaS

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Bourhy, Pascale, Laurence Salaün, Aurélie Lajus, Claudine Médigue, Caroline Boursaux-Eude, and Mathieu Picardeau. "A Genomic Island of the Pathogen Leptospira interrogans Serovar Lai Can Excise from Its Chromosome." Infection and Immunity 75, no. 2 (2006): 677–83. http://dx.doi.org/10.1128/iai.01067-06.

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ABSTRACT An examination of the two Leptospira interrogans genomes sequenced so far reveals few genetic differences, including an extra DNA region, 54 kb in length, in L. interrogans serovar Lai. This locus contains 103 predicted coding sequences that are absent from the genome of L. interrogans serovar Copenhageni, of which only 20% had significant BLASTP hits in GenBank. By analyzing the L. interrogans serovar Lai genome by pulsed-field gel electrophoresis, we also found that this 54-kb DNA fragment exists as a circular plasmid. This was confirmed by amplification of a DNA fragment correspond

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Lobos, Olga, and Carlos Padilla. "Phenotypic characterization and genomic DNA polymorphisms of Escherichia coli strains isolated as the sole micro-organism from vaginal infections." Microbiology 155, no. 3 (2009): 825–30. http://dx.doi.org/10.1099/mic.0.021733-0.

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Vaginal infections such as vulvovaginal candiadiasis, trichomoniasis and bacterial vaginosis are common worldwide. Accurate diagnosis and prescription of appropriate treatments are important since these infections are linked to adverse outcomes for women during pregnancy and for newborns. Several aetiological agents are responsible for these infectious diseases; however, the presence of Escherichia coli in these infections is controversial. Thus, it is important to identify some phenotypic and genotypic properties of E. coli strains isolated from vaginal infections. Forty-six E. coli strains i

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Guyer, Debra M., Jyh-Shyang Kao, and Harry L. T. Mobley. "Genomic Analysis of a Pathogenicity Island in Uropathogenic Escherichia coli CFT073: Distribution of Homologous Sequences among Isolates from Patients with Pyelonephritis, Cystitis, and CatheterAssociated Bacteriuria and from Fecal Samples." Infection and Immunity 66, no. 9 (1998): 4411–17. http://dx.doi.org/10.1128/iai.66.9.4411-4417.1998.

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ABSTRACT Urinary tract infection is the most frequently diagnosed kidney and urologic disease and Escherichia coli is by far the most common etiologic agent. Uropathogenic strains have been shown to contain blocks of DNA termed pathogenicity islands (PAIs) which contribute to their virulence. We have defined one of these regions of DNA within the chromosome of a highly virulentE. coli strain, CFT073, isolated from the blood and urine of a woman with acute pyelonephritis. The 57,988-bp stretch of DNA has characteristics which define PAIs, including a size greater than 30 kb, the presence of ins

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Goodall, Daniel J., Katie H. Jameson, Michelle Hawkins, and Christian J. Rudolph. "A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups." International Journal of Molecular Sciences 22, no. 15 (2021): 7928. http://dx.doi.org/10.3390/ijms22157928.

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Termination of DNA replication, the final stage of genome duplication, is surprisingly complex, and failures to bring DNA synthesis to an accurate conclusion can impact genome stability and cell viability. In Escherichia coli, termination takes place in a specialised termination area opposite the origin. A ‘replication fork trap’ is formed by unidirectional fork barriers via the binding of Tus protein to genomic ter sites. Such a fork trap system is found in some bacterial species, but it appears not to be a general feature of bacterial chromosomes. The biochemical properties of fork trap syst

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Akman, Leyla, Rita V. M. Rio, Charles B. Beard, and Serap Aksoy. "Genome Size Determination and Coding Capacity of Sodalis glossinidius, an Enteric Symbiont of Tsetse Flies, as Revealed by Hybridization to Escherichia coliGene Arrays." Journal of Bacteriology 183, no. 15 (2001): 4517–25. http://dx.doi.org/10.1128/jb.183.15.4517-4525.2001.

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ABSTRACT Recent molecular characterization of various microbial genomes has revealed differences in genome size and coding capacity between obligate symbionts and intracellular pathogens versus free-living organisms. Multiple symbiotic microorganisms have evolved with tsetse fly, the vector of African trypanosomes, over long evolutionary times. Although these symbionts are indispensable for tsetse fecundity, the biochemical and molecular basis of their functional significance is unknown. Here, we report on the genomic aspects of the secondary symbiont Sodalis glossinidius. The genome size ofSo

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Orbach, M. J., W. P. Schneider, and C. Yanofsky. "Cloning of methylated transforming DNA from Neurospora crassa in Escherichia coli." Molecular and Cellular Biology 8, no. 5 (1988): 2211–13. http://dx.doi.org/10.1128/mcb.8.5.2211.

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An arg-2 mutant of Neurospora crassa was transformed to prototrophy with a pBR322-N. crassa genomic DNA library. Repeated attempts to recover the integrated transforming DNA or segments thereof by digestion, ligation, and transformation of Escherichia coli, with selection for the plasmid marker ampicillin resistance, were unsuccessful. Analyses of a N. crassa transformant demonstrated that the introduced DNA was heavily methylated at cytosine residues. This methylation was shown to be responsible for our inability to recover transformants in standard strains of E. coli; transformants were read

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Orbach, M. J., W. P. Schneider, and C. Yanofsky. "Cloning of methylated transforming DNA from Neurospora crassa in Escherichia coli." Molecular and Cellular Biology 8, no. 5 (1988): 2211–13. http://dx.doi.org/10.1128/mcb.8.5.2211-2213.1988.

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An arg-2 mutant of Neurospora crassa was transformed to prototrophy with a pBR322-N. crassa genomic DNA library. Repeated attempts to recover the integrated transforming DNA or segments thereof by digestion, ligation, and transformation of Escherichia coli, with selection for the plasmid marker ampicillin resistance, were unsuccessful. Analyses of a N. crassa transformant demonstrated that the introduced DNA was heavily methylated at cytosine residues. This methylation was shown to be responsible for our inability to recover transformants in standard strains of E. coli; transformants were read

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Jha, Prakash K., and Satyapriya Sarkar. "DNA Sequencing and Comparative Sequence Analysis Reveal that the Escherichia coli Genomic DNA May Replace the Target DNA During Molecular Cloning: Evidence for the Erroneous Assembly of E. coli DNA into Database Sequences." Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 118, no. 2 (1997): 333–39. http://dx.doi.org/10.1016/s0305-0491(97)00175-2.

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33

Alokam, Suneetha, Shu-Lin Liu, Kamal Said, and Kenneth E. Sanderson. "Inversions over the Terminus Region in Salmonella and Escherichia coli: IS200s as the Sites of Homologous Recombination Inverting the Chromosome of Salmonella enterica Serovar Typhi." Journal of Bacteriology 184, no. 22 (2002): 6190–97. http://dx.doi.org/10.1128/jb.184.22.6190-6197.2002.

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ABSTRACT Genomic rearrangements (duplications and inversions) in enteric bacteria such as Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12 are frequent (10−3 to 10−5) in culture, but in wild-type strains these genomic rearrangements seldom survive. However, inversions commonly survive in the terminus of replication (TER) region, where bidirectional DNA replication terminates; nucleotide sequences from S. enterica serovar Typhimurium LT2, S. enterica serovar Typhi CT18, E. coli K12, and E. coli O157:H7 revealed genomic inversions spanning the TER region. Assuming that S. ent

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Handford, Cynthia L., Charma T. Stang, Tracy L. Raivio, and Jonathan J. Dennis. "The contribution of small cryptic plasmids to the antibiotic resistance of enteropathogenic Escherichia coli E2348/69." Canadian Journal of Microbiology 55, no. 11 (2009): 1229–39. http://dx.doi.org/10.1139/w09-079.

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Two uncharacterized small cryptic plasmids (SCPs) were isolated from enteropathogenic Escherichia coli strain E2348/69. Genomic DNA sequence analysis of both SCPs indicated that the smaller plasmid, p5217, encoded several mobilization genes, whereas the larger plasmid, p6148, encoded several putative antibiotic resistance determinants. Complementation analysis showed that p6148 encodes functional streptomycin resistance genes but, owing to the presence of several frameshift mutations, a nonfunctional sulfonamide resistance determinant. A plasmid similar to p6148 has previously been shown to co

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Cockram, Charlotte A., Milana Filatenkova, Vincent Danos, Meriem El Karoui, and David R. F. Leach. "Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo." Proceedings of the National Academy of Sciences 112, no. 34 (2015): E4735—E4742. http://dx.doi.org/10.1073/pnas.1424269112.

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Understanding molecular mechanisms in the context of living cells requires the development of new methods of in vivo biochemical analysis to complement established in vitro biochemistry. A critically important molecular mechanism is genetic recombination, required for the beneficial reassortment of genetic information and for DNA double-strand break repair (DSBR). Central to recombination is the RecA (Rad51) protein that assembles into a spiral filament on DNA and mediates genetic exchange. Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequenc

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Jackson, Scott A., Michael L. Kotewicz, Isha R. Patel, David W. Lacher, Jayanthi Gangiredla, and Christopher A. Elkins. "Rapid Genomic-Scale Analysis of Escherichia coli O104:H4 by Using High-Resolution Alternative Methods to Next-Generation Sequencing." Applied and Environmental Microbiology 78, no. 5 (2011): 1601–5. http://dx.doi.org/10.1128/aem.07464-11.

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ABSTRACTTwo technologies, involving DNA microarray and optical mapping, were used to quickly assess gene content and genomic architecture of recent emergentEscherichia coliO104:H4 and related strains. In real-time outbreak investigations, these technologies can provide congruent perspectives on strain, serotype, and pathotype relationships. Our data demonstrated clear discrimination between clinically, temporally, and geographically distinct O104:H4 isolates and rapid characterization of strain differences.

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Lloyd, Amanda L., David A. Rasko, and Harry L. T. Mobley. "Defining Genomic Islands and Uropathogen-Specific Genes in Uropathogenic Escherichia coli." Journal of Bacteriology 189, no. 9 (2007): 3532–46. http://dx.doi.org/10.1128/jb.01744-06.

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ABSTRACT Uropathogenic Escherichia coli (UPEC) strains are responsible for the majority of uncomplicated urinary tract infections, which can present clinically as cystitis or pyelonephritis. UPEC strain CFT073, isolated from the blood of a patient with acute pyelonephritis, was most cytotoxic and most virulent in mice among our strain collection. Based on the genome sequence of CFT073, microarrays were utilized in comparative genomic hybridization (CGH) analysis of a panel of uropathogenic and fecal/commensal E. coli isolates. Genomic DNA from seven UPEC (three pyelonephritis and four cystitis

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Abulencia, Carl B., Denise L. Wyborski, Joseph A. Garcia, et al. "Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments." Applied and Environmental Microbiology 72, no. 5 (2006): 3291–301. http://dx.doi.org/10.1128/aem.72.5.3291-3301.2006.

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ABSTRACT Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using φ29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting i

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Murshed, Mohammad, Sabeena Shahnaz, and Md Abdul Malek. "Isolation of post operative hospital acquired infections in a private hospital of Bangladesh and identification of clonal relatedness of E. coli by using Pulse filed gel electrophoresis." Bangladesh Journal of Medical Microbiology 6, no. 2 (2012): 7–10. http://dx.doi.org/10.3329/bjmm.v6i2.19369.

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Isolation and identification of post operative hospital acquired infection was carried out from July 2008 to December 2008 in Holy Family Red Crescent Medical College Hospital (private hospital). The major pathogen of wound infection was E. coli. A total; of 120 samples were collected from the surrounding environment of post operative room like floor, bed sheets, instruments, dressing materials, catheter, nasogastric and endotracheal tube. E. coli (40%) was the predominant organism followed by S. aureus (24%). DNA fingerprinting analysis using pulsed field gel electreopheresis of XbaI restrict

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Kim, Sung-Hun, Jeong-Hyun Park, Bok-Kwon Lee, et al. "Complete Genome Sequence of Salmonella Bacteriophage SS3e." Journal of Virology 86, no. 18 (2012): 10253–54. http://dx.doi.org/10.1128/jvi.01550-12.

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ASalmonellalytic bacteriophage, SS3e, was isolated, and its genome was sequenced completely. This phage is able to lyse not only variousSalmonellaserovars but alsoEscherichia coli,Shigella sonnei,Enterobacter cloacae, andSerratia marcescens, indicating a broad host specificity. Genomic sequence analysis of SS3e revealed a linear double-stranded DNA sequence of 40,793 bp harboring 58 open reading frames, which is highly similar toSalmonellaphages SETP13 and MB78.

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Allison, Gwen E., Dario Angeles, Nai Tran-Dinh, and Naresh K. Verma. "Complete Genomic Sequence of SfV, a Serotype-Converting Temperate Bacteriophage of Shigellaflexneri." Journal of Bacteriology 184, no. 7 (2002): 1974–87. http://dx.doi.org/10.1128/jb.184.7.1974-1987.2002.

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ABSTRACT Bacteriophage SfV is a temperate serotype-converting phage of Shigella flexneri. SfV encodes the factors involved in type V O-antigen modification, and the serotype conversion and integration-excision modules of the phage have been isolated and characterized. We now report on the complete sequence of the SfV genome (37,074 bp). A total of 53 open reading frames were predicted from the nucleotide sequence, and analysis of the corresponding proteins was used to construct a functional map. The general organization of the genes in the SfV genome is similar to that of bacteriophage λ, and

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Kazlauskas, Darius, Mart Krupovic, Julien Guglielmini, Patrick Forterre, and Česlovas Venclovas. "Diversity and evolution of B-family DNA polymerases." Nucleic Acids Research 48, no. 18 (2020): 10142–56. http://dx.doi.org/10.1093/nar/gkaa760.

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Abstract B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogen

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Tao, Han, Christoph Bausch, Craig Richmond, Frederick R. Blattner, and Tyrrell Conway. "Functional Genomics: Expression Analysis ofEscherichia coli Growing on Minimal and Rich Media." Journal of Bacteriology 181, no. 20 (1999): 6425–40. http://dx.doi.org/10.1128/jb.181.20.6425-6440.1999.

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ABSTRACT DNA arrays of the entire set of Escherichia coli genes were used to measure the genomic expression patterns of cells growing in late logarithmic phase on minimal glucose medium and on Luria broth containing glucose. Ratios of the transcript levels for all 4,290E. coli protein-encoding genes (cds) were obtained, and analysis of the expression ratio data indicated that the physiological state of the cells under the two growth conditions could be ascertained. The cells in the rich medium grew faster, and expression of the majority of the translation apparatus genes was significantly elev

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Bharti, Sanjay Kumar, and Umesh Varshney. "Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli." Nucleic Acids Research 38, no. 7 (2010): 2291–301. http://dx.doi.org/10.1093/nar/gkp1210.

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González, María Laura, Jorge Chiapella, Juliana Topalian, and Juan Domingo Urdampilleta. "Genomic differentiation of Deschampsia antarctica and D. cespitosa (Poaceae) based on satellite DNA." Botanical Journal of the Linnean Society 194, no. 3 (2020): 326–41. http://dx.doi.org/10.1093/botlinnean/boaa045.

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Abstract Repetitive DNA is a rapidly evolving component of vascular plant genomes, which can account for genomic differentiation in plant lineages. Satellite DNA (satDNA) is tandem repetitive DNA for which array size and disposition on chromosomes may vary between reproductively isolated groups, such as different populations or closely related species. Deschampsia is a cosmopolitan grass genus growing in temperate and cold regions; D. cespitosa is widespread all over the world, whereas D. antarctica is restricted to Antarctica and southern Patagonia. The present work aims to the identification

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KUDUĞ CEYLAN, HÜLYA, YAKUP ULUSU, SEMA BILGIN, and İSA GÖKÇE. "EXPRESSION OF CELLULOSE-DEGRADING ENDOGLUCANASE FROM BACILLUS SUBTILIS USING PTOLT EXPRESSION SYSTEM IN ESCHERICHIA COLI." Cellulose Chemistry and Technology 55, no. 5-6 (2021): 619–27. http://dx.doi.org/10.35812/cellulosechemtechnol.2021.55.50.

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Endoglucanases randomly hydrolyse the cellulose chains by acting upon internal β-1,4-D-glycosidic bonds and are used extensively in industrial applications. In this study, bacterial endoglucanase gene yhfE was obtained by PCR, using primers based on genomic sequences of Bacillus subtilis strains. 1041 bp DNA fragment of yhfE was cloned into Escherichia coli DH5α through the use of pTolT expression plasmid. PCR, restriction enzyme analysis and DNA sequencing were performed in order to confirm the cloning. E. coli BL21-AI cells expressed the yhfE after induction at 0.04% of arabinose concentrati

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MIYAMOTO, TAKAHISA, NATSUKO ICHIOKA, CHIE SASAKI, et al. "Polymerase Chain Reaction Assay for Detection of Escherichia coli O157:H7 and Escherichia coli O157:H−." Journal of Food Protection 65, no. 1 (2002): 5–11. http://dx.doi.org/10.4315/0362-028x-65.1.5.

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The DNA band patterns generated by polymerase chain reaction (PCR) using the du2 primer and template DNAs from various strains of Escherichia coli and non–E. coli bacteria were compared. Among three to five prominent bands produced, the three bands at about 1.8, 2.7, and 5.0 kb were detected in all of the E. coli O157 strains tested. Some nonpathogenic E. coli and all pathogenic E. coli except E. coli O157 showed bands at 1.8 and 5.0 kb. It seems that the band at 2.7 kb is specific to E. coli O157. Sequence analysis of the 2.7-kb PCR product revealed the presence of a DNA sequence specific to

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Nahar, KM, MSR Khan, M. Alam, and MK Nesa. "Escherichia coli from Horses Reared in and around Bangladesh Agricultural University Campus- A Study on Isolation and Characterization." Progressive Agriculture 22, no. 1-2 (2013): 26–35. http://dx.doi.org/10.3329/pa.v22i1-2.16464.

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The present study was conducted with a view to isolate and characterize Escherichia coli (E. coli) from horses reared in and around Bangladesh Agricultural University (BAU) campus and to know the clonal relationship of the isolates with E. coli of cattle, goat and chicken. It also focused on the determination of antimicrobial sensitivity and resistant pattern of the isolated horse E. coli. A total of 10 faecal samples, comprising 4 from diarrhoeic horses and 6 from apparently healthy horses were collected. The overall prevalence of E. coli was recorded as 60%. All isolates fermented dextrose,

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Kuchanny, D., G. Klein, J. Krzewska, A. Czyz, and B. Lipińska. "Cloning of the groE operon of the marine bacterium Vibrio harveyi using a lambda vector." Acta Biochimica Polonica 45, no. 1 (1998): 261–70. http://dx.doi.org/10.18388/abp.1998_4341.

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groES and groEL genes encode two co-operating proteins GroES and GroEL, belonging to a class of chaperone proteins highly conserved during evolution. The GroE chaperones are indispensable for the growth of bacteriophage lambda in Escherichia coli cells. In order to clone the groEL and groES genes of the marine bacterium Vibrio harveyi, we constructed the V. harveyi genomic library in the lambdaEMBL1 vector, and selected clones which were able to complement mutations in both groE genes of E. coli for bacteriophage lambda growth. Using Southern hybridization, in one of these clones we identified

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Chizhikov, Vladimir, Avraham Rasooly, Konstantin Chumakov, and Dan D. Levy. "Microarray Analysis of Microbial Virulence Factors." Applied and Environmental Microbiology 67, no. 7 (2001): 3258–63. http://dx.doi.org/10.1128/aem.67.7.3258-3263.2001.

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ABSTRACT Hybridization with oligonucleotide microchips (microarrays) was used for discrimination among strains of Escherichia coli and other pathogenic enteric bacteria harboring various virulence factors. Oligonucleotide microchips are miniature arrays of gene-specific oligonucleotide probes immobilized on a glass surface. The combination of this technique with the amplification of genetic material by PCR is a powerful tool for the detection of and simultaneous discrimination among food-borne human pathogens. The presence of six genes (eaeA, slt-I,slt-II, fliC, rfbE, andipaH) encoding bacteri

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