Academic literature on the topic 'E. coli Genome'
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Journal articles on the topic "E. coli Genome"
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KRÖGER, MANFRED. "E. coli genome." Nature 339, no. 6223 (June 1989): 330. http://dx.doi.org/10.1038/339330b0.
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Dixit, Purushottam D., Tin Yau Pang, F. William Studier, and Sergei Maslov. "Recombinant transfer in the basic genome ofEscherichia coli." Proceedings of the National Academy of Sciences 112, no. 29 (July 7, 2015): 9070–75. http://dx.doi.org/10.1073/pnas.1510839112.
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An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.
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Cochrane, Ryan R., Stephanie L. Brumwell, Arina Shrestha, Daniel J. Giguere, Samir Hamadache, Gregory B. Gloor, David R. Edgell, and Bogumil J. Karas. "Cloning of Thalassiosira pseudonana’s Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli." Biology 9, no. 11 (October 26, 2020): 358. http://dx.doi.org/10.3390/biology9110358.
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Algae are attractive organisms for biotechnology applications such as the production of biofuels, medicines, and other high-value compounds due to their genetic diversity, varied physical characteristics, and metabolic processes. As new species are being domesticated, rapid nuclear and organelle genome engineering methods need to be developed or optimized. To that end, we have previously demonstrated that the mitochondrial genome of microalgae Phaeodactylum tricornutum can be cloned and engineered in Saccharomyces cerevisiae and Escherichia coli. Here, we show that the same approach can be used to clone mitochondrial genomes of another microalga, Thalassiosira pseudonana. We have demonstrated that these genomes can be cloned in S. cerevisiae as easily as those of P. tricornutum, but they are less stable when propagated in E. coli. Specifically, after approximately 60 generations of propagation in E. coli, 17% of cloned T. pseudonana mitochondrial genomes contained deletions compared to 0% of previously cloned P. tricornutum mitochondrial genomes. This genome instability is potentially due to the lower G+C DNA content of T. pseudonana (30%) compared to P. tricornutum (35%). Consequently, the previously established method can be applied to clone T. pseudonana’s mitochondrial genome, however, more frequent analyses of genome integrity will be required following propagation in E. coli prior to use in downstream applications.
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Zhang, Hui, Yao Xiong, Wenhai Xiao, and Yi Wu. "Investigation of Genome Biology by Synthetic Genome Engineering." Bioengineering 10, no. 2 (February 20, 2023): 271. http://dx.doi.org/10.3390/bioengineering10020271.
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Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design–build–test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and function of genomes, and highlight the unique values of synthetic genomics.
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Dobrindt, Ulrich, Franziska Agerer, Kai Michaelis, Andreas Janka, Carmen Buchrieser, Martin Samuelson, Catharina Svanborg, Gerhard Gottschalk, Helge Karch, and Jörg Hacker. "Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays." Journal of Bacteriology 185, no. 6 (March 15, 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. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA “pathoarray” developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.
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Mori, Hideo, Hiroshi Mizoguchi, and Tatsuro Fujio. "Escherichia coli minimum genome factory." Biotechnology and Applied Biochemistry 46, no. 3 (March 1, 2007): 157. http://dx.doi.org/10.1042/ba20060107.
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Hayashi, Tetsuya. "Genome plasticity of Escherichia coli; insights from genome analysis." Environmental Mutagen Research 27, no. 2 (2005): 117–18. http://dx.doi.org/10.3123/jems.27.117.
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Cui, Tailin, Naoki Moro‐oka, Katsufumi Ohsumi, Kenichi Kodama, Taku Ohshima, Naotake Ogasawara, Hirotada Mori, Barry Wanner, Hironori Niki, and Takashi Horiuchi. "Escherichia coli with a linear genome." EMBO reports 8, no. 2 (January 12, 2007): 181–87. http://dx.doi.org/10.1038/sj.embor.7400880.
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Kolisnychenko, V. "Engineering a Reduced Escherichia coli Genome." Genome Research 12, no. 4 (April 1, 2002): 640–47. http://dx.doi.org/10.1101/gr.217202.
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KOOB, MICHAEL D., ANITA J. SHAW, and DOUGLAS C. CAMERON. "Minimizing the Genome of Escherichia coli." Annals of the New York Academy of Sciences 745, no. 1 (December 17, 2006): 1–3. http://dx.doi.org/10.1111/j.1749-6632.1994.tb44359.x.
Full textDissertations / Theses on the topic "E. coli Genome"
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Patel, Muneeza S. "Algorithms for E. coli genome engineering." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/106461.
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Thesis: M. Eng. in Computer Science & Molecular Biology, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
"June 2016." Page 90 blank. Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 70-72).
Author summary: Lamba red recombineering is one of methods of performing genome engineering. However, this method of genome editing is not very specific and efficient and is highly dependent on the genomic regions that are targeted (integration sites). In this project we explored ways of identifying what makes a site well suited for lambda red genome engineering. We wanted to explore whether we can eventually predict the "goodness" of an integration site using an algorithm. Our initial approach to the problem was to write an algorithm based on some characteristics that we felt would be key to determining the goodness of a site. Choosing to initially focus on specificity of the integrations, we used experimental approaches to evaluate whether our algorithm had any predictive powers for specificity. Upon failing, we revised our plan to generate a dataset of ~150 sites and their integration data (whether integration was successful, specific and efficient at that site). We used this dataset to explore correlations between the specificity data and characteristics we thought might affect the specificity of sites. The most promising characteristics appeared to be the uniqueness of the genomic site (as determined by BLAST) and the existence of Repetitive Extragenic Palindrome (REP) sites at the site of integration. Section I of this thesis sets up the problem, section II talks about the initial approach we took to the problem and section III discusses our modified approach -- which formed the bulk of this thesis project. Section I and III are the most relevant to understand the project, while Section II gives more content to the project in addition to detailed insight to what approaches did not work.
by Muneeza S. Patel.
M. Eng. in Computer Science & Molecular Biology
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Neelakanta, Girish. "Genome variations in commensal and pathogenic E.coli." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974330329.
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Schlegel, Susan. "From protein production to genome evolution in Escherichia coli." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-94993.
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The aim of my Ph.D. studies was to improve production yields of membrane- and secretory proteins in the widely used E. coli protein production strain BL21(DE3). In this strain expression of the gene encoding the protein of interest is driven by the powerful T7 RNA polymerase (T7 RNAP) whose gene is located on the chromosome and under control of the strong, IPTG-inducible lacUV5 promoter. Unfortunately, the production of many membrane and secretory proteins is 'toxic' to BL21(DE3), resulting in poor growth and low production yields. To understand this ‘toxicity’, the BL21(DE3) derived mutant strains C41(DE3) and C43(DE3) were characterized. Somehow, these strains can efficiently produce many ‘toxic’ membrane and secretory proteins. We showed that mutations weakening the lacUV5 promoter are responsible for this. These mutations result in a slower onset of protein production upon the addition of IPTG, which avoids saturating the Sec-translocon capacity. The Sec-translocon is a protein-conducting channel in the cytoplasmic membrane mediating the biogenesis of membrane proteins and translocation of secretory proteins. Next, we constructed a BL21(DE3)-derivative, Lemo21(DE3), in which the activity of T7 RNAP can be precisely controlled by titrating in its natural inhibitor T7 lysozyme using the rhamnose promoter system. In Lemo21(DE3), the expression level of genes encoding membrane and secretory proteins can be set such that the Sec-translocon capacity is not saturated. This is key to optimizing membrane and secretory protein production yields. Finally, reconstructing the evolution of C41(DE3) from BL21(DE3) in real time showed that during its isolation C41(DE3) had acquired mutations critical for surviving the starvation conditions used, and provided insight in how the mutations in the lacUV5 promoter had occurred.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.
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Wlodarski, Michal. "Dynamics of E. coli genome and cytosol under antibiotics." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275205.
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In light of an urgent need for improved antimicrobial diagnostics and therapeutics, understanding bacterial behaviour, and bacterial responses to treatments in particular, is one of the key objectives of modern medical research. While the molecular mode of action of antibiotics is usually well known, their effect on the cell at a "systems" level (on the regulatory networks, metabolism, etc.) is only beginning to be quantitatively understood. We address some of these response phenotypes in Escherichia coli testing different antibiotic classes and growth conditions. We study the short (< 15 s) time-scale fluctuation dynamics of fluorescently-tagged chromosomal loci and cytosolic aggregates, which report for the state of locus ”compaction” and the levels of macromolecular crowding of the cytosol, respectively. We improve the precision of those measurements developing a novel data treatment procedure and discover that sub-lethal doses of ciprofloxacin, rifampicin, and vancomycin as well as hyperosmotic shock conditions cause small but consistent changes (unique to each treatment agent) to the physical organisation of chromosomal Ori2 and Ter3 loci and the cytosol. We reveal, among other findings, strong correlations between the effects in different parts of the chromosome and between the chromosome and cytosol. In addition, we complement the marker dynamics work with single-cell level gene expression measurements during sub-lethal translation inhibition. Specifically, we compare responses to tetracycline and chloramphenicol from constitutive and ribosomal promoters in Ori3 and Ter3 chromosomal positions over long (7 h) treatment times in exponentially growing bacteria. We reveal, for the first time, the kinetics of cellular resource allocation and provide novel insights on globally regulated transcription, relevant to the three-component proteome partitioning model, gene-length dependent effects of the processivity of translation, and ”reversibility” of ribosome-binding antibiotics. In addition, we discover a strong correlation between the timing of responses from promoters in the Ori3 and Ter3 positions, and a small but consistent difference in the response magnitude between the two positions.
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Romero, Alvarez David. "Genome wide analyses of the Escherichia coli primary and secondary transcriptomes." Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/6917/.
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Escherichia coli K12 serves as an important model for studying systems that are important to bacteria in their own right as well as those that are conserved in ‘higher' organisms, which are more difficult and costly to study. Like many model organisms, the genome of K12 has been sequenced, producing a catalogue of protein-coding and stable-RNA genes that enabled study using ‘omic’ approaches. This has led to a rapid expansion of our knowledge of patterns of gene expression and their dependency on growth conditions, cell physiology and individual genes. However, the underlying networks of gene regulation are less well understood, but are known to involve the control of steps in RNA processing and degradation as well as transcription and translation. With this in mind, this thesis describes the development of an approach based on RNA sequencing that produces nucleotide-resolution transcriptome maps that distinguish sites that correspond to RNA processing and steps in degradation from those of transcription initiation, while incorporating all classes of RNA. Comparison with results obtained previously validated the approach, which has been applied already to the study of other bacterial species. Within the E. coli map, many new features were identified, such as previously undetected small RNAs and processing at a site associated with the production of specialised ribosomes, which may ensure the translation of leaderless mRNAs, which were also mapped. The approach also showed the benefit of incorporating steps that can differentiate the 5’ status of transcripts in assigning sites of transcription initiation. RNA sequencing was also used to map sites of cleavage by RNase E, an essential endoribonuclease that is central to both the processing and degradation of RNA in bacteria and plant plastids. This aspect of the thesis has advanced from pilot studies to the point where the ‘code’ that determines one form of substrate recognition by RNase E is beginning to emerge. As a result of this success, equivalent data has been collected for other ribonucleases involved in RNA processing and degradation. Continuing analysis of the primary and secondary transcriptomes, consisting of native, unprocessed transcripts and of transcripts that have been modified from their native form via processing and/or degradation respectively, with the tools presented here promises to broaden and deepen our understanding of an important model organism.
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Coss, Dennis. "Insertion of genes and operons into the Escherichia coli genome through targeted recombination." Morgantown, W. Va. : [West Virginia University Libraries], 2005. https://eidr.wvu.edu/etd/documentdata.eTD?documentid=3804.
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Thesis (Ph. D.)--West Virginia University, 2005.Title from document title page. Document formatted into pages; contains v, 125 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 71-87).
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Mosberg, Joshua Adam Weintrob. "Studying and Improving Lambda Red Recombination for Genome Engineering in Escherichia coli." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10777.
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The phage-derived Lambda Red recombination system utilizes exogenous DNA in order to generate precise insertion, deletion, and point mutations in Escherichia coli and other bacteria. Due to its convenience, it is a frequently-used tool in genetics and molecular biology, as well as in larger-scale genome engineering projects. However, limited recombination frequency constrains the usefulness of Lambda Red for several important applications. In this work, I utilize a mechanism-guided approach in order to improve the power and utility of Lambda Red recombination.
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El, Sayyed Hafez. "Mapping Topoisomerase IV Binding and Activity Sites on the E. coli genome." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS362/document.
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Des liens de caténation sont progressivement crées lors de la réplication de l’ADN et sont responsables de la cohésion des chromatides sœurs. La topoisomérase IV est une topoisomérase de type II impliquée dans la résolution de ces liens de caténation accumulés derrière la fourche de réplication, et lors de la dernière étape de séparation des chromatides sœurs à la fin de la réplication. Nous avons étudié la liaison de la topoIV à l’ADN ainsi que son activité catalytique à l’aide de méthodes de biologie moléculaire et de génomique. Une expérience de ChIPseq a révélé que l’interaction de la topoIV de chez E.coli avec l’ADN est contrôlée par la réplication. Durant la réplication, la topoIV a accès à des centaines de sites sur l’ADN mais ne se lie qu’à quelques sites où elle exerce son activité catalytique. La conformation locale de la chromatine et l’expression des gènes influencent la sélection de certains sites. De plus, une forte liaison et une activité catalytique renforcée a été trouvée au site de résolution des dimers, dif. Le site dif est situé à l’opposé de l’origine de réplication dans le macrodomaine ter. Nous avons montré qu’il existe une interaction physique et fonctionnelle entre la topoIV et la recombinase XerCD, qui agit au site dif. Cette interaction est médiée par MatP, une protéine essentielle dans l’organisation du macrodomaine ter. L’ensemble de ces résultats montre que la topoIV, XerCD/dif et MatP œuvrent ensemble pour permettre l’étape finale de ségrégation des chromosomes lors du cycle cellulaireCatenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle
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Johnson, Matthew David. "Understanding the regulation of acid resistance in E. coli using whole genome techniques." Thesis, University of Birmingham, 2011. http://etheses.bham.ac.uk//id/eprint/3006/.
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The ability of bacteria to thrive in a variety of host environments depends on their capacity to sense and respond to a wide array of stressors. E. coli encounters many stresses during transit through the gastro-intestinal tract, including acid stress. Acid stress response in E. coli is regulated by a complex network called AR2. The AR2 network comprises several local regulators that collate signals from multiple two-component systems (TCS) including RcsBD, EvgAS and PhoPQ. We combined lab-based evolution and whole genome re-sequencing to generate and identify mutations that confer increased acid resistance in E. coli K-12. All of these mutations map in the gene encoding EvgS, the sensor kinase of the EvgAS TCS. Using a luciferase reporter system and phenotypic assays we characterised the nature of these evgS mutations and their contribution to acid resistance. We also used high-temporal resolution luciferase reporter assays to uncover novel aspects of this network and implicate PhoP in the repression of acid resistance. Finally, we used our evgS mutants to characterise novel interactions within the AR2 network between the two component systems RcsBD and EvgAS. These results are discussed in relation to the role of regulatory networks in bacteria.
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Schmidt, Dorothea. "Molekulare Analyse des probiotischen Stamms Escherichia coli Nissle 1917." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2009. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1243973355362-88295.
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Der probiotische Stamm E. coli Nissle 1917 ist ein Fäkalisolat, das in der Medizin traditionell zur Behandlung verschiedener gastrointestinaler Erkrankungen eingesetzt wird. Durch erfolgversprechende klinische Studien zur Remissionserhaltung bei Colitis ulcerosa, bei denen EcN als therapeutische Alternative zur Standardmedikation eingesetzt wird, ist das Interesse an den Wirkmechanismen von Probiotika stark gestiegen. EcN gehört derzeit zu den am besten untersuchten Probiotika. Einige Wirkmechanismen konnten dadurch schon aufgeklärt werden. So sind vermutlich Strukturkomponenten und stammspezifische Syntheseleistungen an der Ausprägung des probiotischen Phänotyps von EcN beteiligt. Schlüssige Konzepte, die über Gene, Genprodukte und molekulare Mechanismen den probiotischen Effekt von EcN erklären, fehlen bislang. Im Rahmen dieser Arbeit wird das Genom von EcN analysiert und auf der Basis der Genomsequenz mit anderen E. coli-Stämmen verglichen. Mit Hilfe einer Promotor-Reporter-Fusionsbibliothek (Promotorbank) werden intestinal in vivo regulierte Gene identifiziert und dadurch neue Ansätze zur Untersuchung der probiotischen Eigenschaften von EcN geschaffen. Die Grundlage für die molekulare Analyse von EcN ist die manuelle Nachannotation seines sequenzierten Genoms. Die EcN-Sequenz wird mit 13 weiteren annotierten E. coli-Sequenzen verglichen. Nach dieser Analyse kodiert EcN derzeit 121 stammspezifische Gene. Die Genomstruktur ist mit den enthaltenen genomischen Inseln und Prophagen dem Genom des uropathogenen E. coli CFT073 sehr ähnlich. Mit wenigen Ausnahmen kodiert EcN alle in E. coli CFT073 vorhandenen Virulenz- und Fitnessfaktoren, so dass auf der Nukleotidebene die nahe Verwandschaft dieser beiden Stämme bestätigt werden kann. Zudem kann gezeigt werden, dass EcN in artifiziellen Systemen wie der Zellkultur oder gnotobiotischen Mäusen ein pathogenes Potenzial hat, obgleich die Kolonisierungsfähigkeit pathogener Bakterien durch Inkubation mit EcN herabgesetzt wird. Eine wichtige Rolle bei der Besiedlung des Intestinaltrakts und der Immunstimulation von Darmepithelzellen spielt auch die globale Regulation der Genaktivität bei EcN durch den alternativen Sigma-Faktor RpoS, der im Gegensatz zu rpoS-Deletionsmutanten zu einer gesteigerten mRNA-Expression des Tight-junction Proteins ZO-1 führt. Des Weiteren führte die Untersuchung von EcN-Deletionsmutanten zu der Schlussfolgerung, dass einige genomische Inseln für Eigenschaften, die das probiotische Verhalten erklären können, eine Rolle spielen. Durch den Einsatz einer Promotorbank von EcN in konventionellen und gnotobiotischen Mäusen werden erstmalig Sequenzen von intestinal in vivo aktiven Promotoren identifiziert. Der Aufbau eines Promotor-Reportergen-Assays mit dem Biolumineszenz erzeugenden luxCDABE-Operon ermöglichte die Untersuchung ausgewählter Promotoren in vitro. Mit einem In Vivo Imaging System (IVIS) kann in weiteren Experimenten die Aktivität dieser Promotoren in lebenden Mäusen untersucht werden. Im Rahmen dieser Arbeit wird gezeigt, dass EcN kein vollkommen harmloser probiotischer Stamm ist. Weitere Informationen über EcN sind dehalb wichtig für eine optimierte Anwendung als Therapeutikum. Die molekulare Analyse ist somit eine unbedingt notwendige Grundlage für weiterführende Untersuchungen der Eigenschaften von EcN, die für seinen probiotischen Charakter verantwortlich sindThe probiotic E. coli Nissle 1917 is a fecal isolate which is traditionally used for treatment of various gastrointestinal disorders. In clinical trials where EcN was used as therapeutic alternative for remission maintenance of ulcerative colitis compared to standard medication, promising results led to an increased interest in probiotics. Today, EcN is one of the best studied probiotics. Therefore, several mechanisms of action could be enlightened. Structural components and strain-specific products are responsible for its probiotic effects. But conclusive concepts about genes, gene products and molecular mechanisms that really contribute to the probiotic character of EcN have not been offered so far. In order to create new possibilities to elucidate the probiotic traits of EcN the genome is analysed by taking this as a basis for comparison to other E. coli genomes and identification of intestinal in vivo regulated genes using a promoter-trap-library. The sequenced EcN genome is annotated and compared to 13 other so far annotated E. coli genomes. Concerning these analyses EcN encodes 121 strain-specific genes. The genome structure including the genomic islands and prophages is highly homolog to the uropathogenic E. coli CFT073. EcN encodes most of the virulence and fitness factors that are present in E. coli CFT073. Therefore, the close relationship of these two strains is confirmed at nucleotide level. Furthermore, it is shown that in artificial systems like cell culture assays and gnotobiotic mice EcN reveals a pathogenic potential although EcN is able to decrease colonization efficiency of pathogenic bacteria. The alternative sigma factor RpoS that is responsible for global regulation and activity of several genes seems to play an important role during colonization of EcN in the intestine and its immunostimulatory effects on intestinal epithelial cells. Investigation of EcN-deletion mutants lacking genomic islands and prophages lead to the conclusion that some genomic islands may play a role for specific probiotic traits. This is the first time where a promoter-trap-library was used in conventional and gnotobiotic mice for collection of intestinal in vivo active promoters. Constructing and establishing a promoter-reporter gene assay with the bioluminescent luxCDABE operon made the investigation of selected promoters in vitro possible as well as establishing a bioluminescence assay using an In Vivo Imaging System (IVIS) for investigation of promoter activity in living mice. In this research project was shown that EcN is not a completely harmless probiotic. The genome structure and regulatory mechanisms of gene expression are the strain’s molecular traits that lead to probiotic activity and immunostimulatory effects. Therefore, the molecular analyses presented here, together with the complete genome sequence, are a basis for further investigations of mechanisms that are responsible for the probiotic effects of EcN
Books on the topic "E. coli Genome"
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Richardson, Deborah Y. Plant genome: Breeding for cold tolerance in plants : January 1987 - April 1992. Beltsville, Md: National Agricultural Library, 1992.
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Vaillancourt, Peter E. E. coli gene expression protocols. Totowa, N.J: Humana, 2011.
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De-Coll', Pier Tancredi. Pier Tancredi De-Coll'. Pistoia: Gli ori, 2018.
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De-Coll', Pier Tancredi. Pier Tancredi De-Coll': Lessico quotidiano. Pistoia: Gli Ori, 2019.
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Heterologous gene expression in E. coli: Methods and protocols. New York, NY: Humana Press, 2011.
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Magnusson, Lisa. Global regulation of gene expression in Escherichia coli: The role of ppGpp, DksA, and the levels of RNA polymerase. Göteborg: Göteborgs universitet, 2007.
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Magnusson, Lisa. Global regulation of gene expression in Escherichia coli: The role of ppGpp, DksA, and the levels of RNA polymerase. Göteborg: Göteborgs universitet, 2007.
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Life on Ice: A History of New Uses for Cold Blood. Chicago: University of Chicago Press, 2017.
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P, Smith C., Rench Jonny, and Brosseau Pat, eds. The programme. La Jolla, CA: Wildstorm, 2008.
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Cold Spring Harbor Meeting on Cancer Cells (3rd 1985). Abstracts of papers presented at the third Cold Spring Harbor Meeting on Cancer Cells: DNA tumor viruses : control of gene expression and replication, September 4-September 8, 1985. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory, 1985.
Find full textBook chapters on the topic "E. coli Genome"
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Milkman, Roger. "Gene Transfer in Escherichia coli." In Organization of the Prokaryotic Genome, 291–309. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818180.ch16.
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Bergthorsson, Ulfar, and Howard Ochman. "Evolution of the E. coli Genome." In Bacterial Genomes, 177–86. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-6369-3_17.
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Jensen, Sheila Ingemann, and Alex Toftgaard Nielsen. "Multiplex Genome Editing in Escherichia coli." In Methods in Molecular Biology, 119–29. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7295-1_8.
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Weinstock, George M. "Resources for the Escherichia coli Genome Project." In Bacterial Genomes, 489–97. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-6369-3_38.
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Fehér, Tamás, Ildikó Karcagi, Zsuzsa Győrfy, Kinga Umenhoffer, Bálint Csörgő, and György Pósfai. "Scarless Engineering of the Escherichia coli Genome." In Microbial Gene Essentiality: Protocols and Bioinformatics, 251–59. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-321-9_16.
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Mellmann, Alexander, Martina Bielaszewska, and Helge Karch. "Genotypic Changes in Enterohemorrhagic Escherichia coli During Human Infection." In Genome Plasticity and Infectious Diseases, 16–26. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555817213.ch2.
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Hall, Barry G. "Transposable elements as activators of cryptic genes in E. coli." In Transposable Elements and Genome Evolution, 181–87. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4156-7_20.
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Labedan, Bernard, and Monica Riley. "Genetic Inventory: Escherichia coli as a Window on Ancestral Proteins." In Organization of the Prokaryotic Genome, 311–29. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818180.ch17.
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Nouwens, Amanda S., Femia G. Hopwood, Mathew Traini, Keith L. Williams, and Bradley J. Walsh. "Proteome Approach to the Identification of Cellular Escherichia coli Proteins." In Organization of the Prokaryotic Genome, 331–46. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818180.ch18.
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Anazawa, Hideharu. "The Concept of the Escherichia coli Minimum Genome Factory." In Microbial Production, 25–32. Tokyo: Springer Japan, 2014. http://dx.doi.org/10.1007/978-4-431-54607-8_3.
Full textConference papers on the topic "E. coli Genome"
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Huang, Yi. "Codon Effect on the Entire Genome Based upon Genome-Wide Recoded Escherichia coli." In 2021 IEEE 9th International Conference on Bioinformatics and Computational Biology (ICBCB). IEEE, 2021. http://dx.doi.org/10.1109/icbcb52223.2021.9459235.
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Kurmi, Annushree, Debashis Das, Piyali Sen, Suvendra Kumar Ray, and Siddhartha Sankar Satapathy. "Gene Essentiality Mediated Base Substitution in Escherichia coli genome: Machine Learning Analysis." In 2022 International Interdisciplinary Conference on Mathematics, Engineering and Science (MESIICON). IEEE, 2022. http://dx.doi.org/10.1109/mesiicon55227.2022.10093501.
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"Impact of negative feedbacks on de novo pyrimidines biosynthesis in E. coli." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-115.
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Meizhen Ji, Jun Lu, Ying Zhang, Changjiang Ding, Dandan Qin, and Haiyan Bai. "Operon prediction based on quadratic discriminant analysis in Escherichia coli genome." In 2010 2nd International Conference on Information Science and Engineering (ICISE). IEEE, 2010. http://dx.doi.org/10.1109/icise.2010.5689023.
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Jia, Mengwen, and Yong Zhan. "Relationship of ORF length and mRNA degradation in Escherichia coli genome." In NUMERICAL ANALYSIS AND APPLIED MATHEMATICS ICNAAM 2012: International Conference of Numerical Analysis and Applied Mathematics. AIP, 2012. http://dx.doi.org/10.1063/1.4756461.
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Vilkhovoy, M., N. Horvath, and J. D. Varner. "Toward genome scale modeling of Escherichia coli cell-free protein synthesis." In IET/SynbiCITE Engineering Biology Conference. Institution of Engineering and Technology, 2016. http://dx.doi.org/10.1049/cp.2016.1253.
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"Impact of terahertz irradiation on the antimicrobial resistance of Escherichia coli JM 103." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-316.
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Wijeratne, Shalini. "A Comparative Analysis of Nanoluc Luciferase and Alkaline Phosphatase as Reporter Proteins for Phage-based Pathogen Detection." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/iibu6123.
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Rapid and specific detection of pathogenic bacteria in food and water sources can be crucial to disease diagnosis and prevention. Genetically modified bacteriophage-based assays are a promising alternative over standard overnight culture-based assays as they can provide comparatively rapid detection. Bacteriophage (phage) viruses specifically infect live bacterial cells for the rapid replication of their viral genome. Scientists exploit this in-built molecular amplification system by genetically modifying phage genes to express certain reporter proteins during an infection. The expression of reporter proteins is confirmed through enzymatic and/or sensory assays, indicating the presence of the pathogenic bacteria. The sensitivity of the reporter phage assays depend on the ability of the genetically engineered phage to successfully express its reporter protein with conserved activity. In this study, we compared two enzymes, alkaline phosphatase (ALP) and nanoluc luciferase (NLuc) as reporter proteins in the context of the above criteria. We genetically modified T7 phage genome to overexpress these enzymes upon infecting BL21 E. coli cells. The reporter proteins were quantified and detected by measuring its luminescence activities. NLuc phage was significantly better at its gene expression in comparison to ALP phage, averaging at 9.8 × 105 molecules of protein/CFU of E. coli and providing a limit of detection at 107 CFU of E. coli/mL. On the other hand, ALP phage was only able to produce 8.6 × 104 molecules of protein/CFU of E. coli and provide a limit of detection at 109 CFU of E. coli/mL. These findings will allow researchers to select their choice of reporter proteins to improve phage-based assays and continue their progress in the field of pathogen detection.
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"On the question of activity of oxidative branch of pentose phosphate shunt in pgl mutant of Escherichia coli." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-311.
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Teramoto, Jun, Kayoko Yamada, Naoki Kobayashi, Ayako Kori, Shige H. Yoshimura, Kunio Takeyasu, and Akira Ishihama. "Anaerobiosis-induced novel nucleoid protein of Escherichia coli: Architectural role in genome DNA compaction." In 2009 International Symposium on Micro-NanoMechatronics and Human Science (MHS). IEEE, 2009. http://dx.doi.org/10.1109/mhs.2009.5351819.
Full textReports on the topic "E. coli Genome"
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Shpigel, Nahum Y., Ynte Schukken, and Ilan Rosenshine. Identification of genes involved in virulence of Escherichia coli mastitis by signature tagged mutagenesis. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699853.bard.
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Mastitis, an inflammatory response of the mammary tissue to invading pathogenic bacteria, is the largest health problem in the dairy industry and is responsible for multibillion dollar economic losses. E. coli are a leading cause of acute mastitis in dairy animals worldwide and certainly in Israel and North America. The species E. coli comprises a highly heterogeneous group of pathogens, some of which are commensal residents of the gut, infecting the mammary gland after contamination of the teat skin from the environment. As compared to other gut microflora, mammary pathogenic E. coli (MPEC) may have undergone evolutionary adaptations that improve their fitness for colonization of the unique and varied environmental niches found within the mammary gland. These niches include competing microbes already present or accompanying the new colonizer, soluble and cellular antimicrobials in milk, and the innate immune response elicited by mammary cells and recruited immune cells. However, to date, no specific virulence factors have been identified in E. coli isolates associated with mastitis. The original overall research objective of this application was to develop a genome-wide, transposon-tagged mutant collection of MPEC strain P4 and to use this technology to identify E. coli genes that are specifically involved in mammary virulence and pathogenicity. In the course of the project we decided to take an alternative genome-wide approach and to use whole genomes bioinformatics analysis. Using genome sequencing and analysis of six MPEC strains, our studies have shown that type VI secretion system (T6SS) gene clusters were present in all these strains. Furthermore, using unbiased screening of MPEC strains for reduced colonization, fitness and virulence in the murine mastitis model, we have identified in MPEC P4-NR a new pathogenicity island (PAI-1) encoding the core components of T6SS and its hallmark effectors Hcp, VgrG and Rhs. Next, we have shown that specific deletions of T6SS genes reduced colonization, fitness and virulence in lactating mouse mammary glands. Our long-term goal is to understand the molecular mechanisms of host-pathogen interactions in the mammary gland and to relate these mechanisms to disease processes and pathogenesis. We have been able to achieve our research objectives to identify E. coli genes that are specifically involved in mammary virulence and pathogenicity. The project elucidated a new basic concept in host pathogen interaction of MPEC, which for the best of our knowledge was never described or investigated before. This research will help us to shed new light on principles behind the infection strategy of MPEC. The new targets now enable prevalence and epidemiology studies of T6SS in field strains of MPEC which might unveil new geographic, management and ecological risk factors. These will contribute to development of new approaches to treat and prevent mastitis by MPEC and perhaps other mammary pathogens. The use of antibiotics in farm animals and specifically to treat mastitis is gradually precluded and thus new treatment and prevention strategies are needed. Effective mastitis vaccines are currently not available, structural components and effectors of T6SS might be new targets for the development of novel vaccines and therapeutics.
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McCarthy, Noel, Eileen Taylor, Martin Maiden, Alison Cody, Melissa Jansen van Rensburg, Margaret Varga, Sophie Hedges, et al. Enhanced molecular-based (MLST/whole genome) surveillance and source attribution of Campylobacter infections in the UK. Food Standards Agency, July 2021. http://dx.doi.org/10.46756/sci.fsa.ksj135.
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This human campylobacteriosis sentinel surveillance project was based at two sites in Oxfordshire and North East England chosen (i) to be representative of the English population on the Office for National Statistics urban-rural classification and (ii) to provide continuity with genetic surveillance started in Oxfordshire in October 2003. Between October 2015 and September 2018 epidemiological questionnaires and genome sequencing of isolates from human cases was accompanied by sampling and genome sequencing of isolates from possible food animal sources. The principal aim was to estimate the contributions of the main sources of human infection and to identify any changes over time. An extension to the project focussed on antimicrobial resistance in study isolates and older archived isolates. These older isolates were from earlier years at the Oxfordshire site and the earliest available coherent set of isolates from the national archive at Public Health England (1997/8). The aim of this additional work was to analyse the emergence of the antimicrobial resistance that is now present among human isolates and to describe and compare antimicrobial resistance in recent food animal isolates. Having identified the presence of bias in population genetic attribution, and that this was not addressed in the published literature, this study developed an approach to adjust for bias in population genetic attribution, and an alternative approach to attribution using sentinel types. Using these approaches the study estimated that approximately 70% of Campylobacter jejuni and just under 50% of C. coli infection in our sample was linked to the chicken source and that this was relatively stable over time. Ruminants were identified as the second most common source for C. jejuni and the most common for C. coli where there was also some evidence for pig as a source although less common than ruminant or chicken. These genomic attributions of themselves make no inference on routes of transmission. However, those infected with isolates genetically typical of chicken origin were substantially more likely to have eaten chicken than those infected with ruminant types. Consumption of lamb’s liver was very strongly associated with infection by a strain genetically typical of a ruminant source. These findings support consumption of these foods as being important in the transmission of these infections and highlight a potentially important role for lamb’s liver consumption as a source of Campylobacter infection. Antimicrobial resistance was predicted from genomic data using a pipeline validated by Public Health England and using BIGSdb software. In C. jejuni this showed a nine-fold increase in resistance to fluoroquinolones from 1997 to 2018. Tetracycline resistance was also common, with higher initial resistance (1997) and less substantial change over time. Resistance to aminoglycosides or macrolides remained low in human cases across all time periods. Among C. jejuni food animal isolates, fluoroquinolone resistance was common among isolates from chicken and substantially less common among ruminants, ducks or pigs. Tetracycline resistance was common across chicken, duck and pig but lower among ruminant origin isolates. In C. coli resistance to all four antimicrobial classes rose from low levels in 1997. The fluoroquinolone rise appears to have levelled off earlier and among animals, levels are high in duck as well as chicken isolates, although based on small sample sizes, macrolide and aminoglycoside resistance, was substantially higher than for C. jejuni among humans and highest among pig origin isolates. Tetracycline resistance is high in isolates from pigs and the very small sample from ducks. Antibiotic use following diagnosis was relatively high (43.4%) among respondents in the human surveillance study. Moreover, it varied substantially across sites and was highest among non-elderly adults compared to older adults or children suggesting opportunities for improved antimicrobial stewardship. The study also found evidence for stable lineages over time across human and source animal species as well as some tighter genomic clusters that may represent outbreaks. The genomic dataset will allow extensive further work beyond the specific goals of the study. This has been made accessible on the web, with access supported by data visualisation tools.
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Willis, C., F. Jorgensen, S. A. Cawthraw, H. Aird, S. Lai, M. Chattaway, I. Lock, E. Quill, and G. Raykova. A survey of Salmonella, Escherichia coli (E. coli) and antimicrobial resistance in frozen, part-cooked, breaded or battered poultry products on retail sale in the United Kingdom. Food Standards Agency, May 2022. http://dx.doi.org/10.46756/sci.fsa.xvu389.
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Frozen, breaded, ready-to-cook chicken products have been implicated in outbreaks of salmonellosis. Some of these outbreaks can be large. For example, one outbreak of Salmonella Enteritidis involved 193 people in nine countries between 2018 and 2020, of which 122 cases were in the UK. These ready-to-cook products have a browned, cooked external appearance, which may be perceived as ready-to-eat, leading to mishandling or undercooking by consumers. Continuing concerns about these products led FSA to initiate a short-term (four month), cross-sectional surveillance study undertaken in 2021 to determine the prevalence of Salmonella spp., Escherichia coli and antimicrobial resistance (AMR) in frozen, breaded or battered chicken products on retail sale in the UK. This study sought to obtain data on AMR levels in Salmonella and E. coli in these products, in line with a number of other FSA instigated studies of the incidence and nature of AMR in the UK food chain, for example, the systematic review (2016). Between the beginning of April and the end of July 2021, 310 samples of frozen, breaded or battered chicken products containing either raw or partly cooked chicken, were collected using representative sampling of retailers in England, Wales, Scotland and Northern Ireland based on market share data. Samples included domestically produced and imported chicken products and were tested for E. coli (including extended-spectrum beta-lactamase (ESBL)-producing, colistin-resistant and carbapenem-resistant E. coli) and Salmonella spp. One isolate of each bacterial type from each contaminated sample was randomly selected for additional AMR testing to determine the minimum inhibitory concentration (MIC) for a range of antimicrobials. More detailed analysis based on Whole Genome Sequencing (WGS) data was used to further characterise Salmonella spp. isolates and allow the identification of potential links with human isolates. Salmonella spp. were detected in 5 (1.6%) of the 310 samples and identified as Salmonella Infantis (in three samples) and S. Java (in two samples). One of the S. Infantis isolates fell into the same genetic cluster as S. Infantis isolates from three recent human cases of infection; the second fell into another cluster containing two recent cases of infection. Countries of origin recorded on the packaging of the five Salmonella contaminated samples were Hungary (n=1), Ireland (n=2) and the UK (n=2). One S. Infantis isolate was multi-drug resistant (i.e. resistant to three different classes of antimicrobials), while the other Salmonella isolates were each resistant to at least one of the classes of antimicrobials tested. E. coli was detected in 113 samples (36.4%), with counts ranging from <3 to >1100 MPN (Most Probable Number)/g. Almost half of the E. coli isolates (44.5%) were susceptible to all antimicrobials tested. Multi-drug resistance was detected in 20.0% of E. coli isolates. E. coli isolates demonstrating the ESBL (but not AmpC) phenotype were detected in 15 of the 310 samples (4.8%) and the AmpC phenotype alone was detected in two of the 310 samples (0.6%) of chicken samples. Polymerase Chain Reaction (PCR) testing showed that five of the 15 (33.3%) ESBL-producing E. coli carried blaCTX-M genes (CTX-M-1, CTX-M-55 or CTX-M-15), which confer resistance to third generation cephalosporin antimicrobials. One E. coli isolate demonstrated resistance to colistin and was found to possess the mcr-1 gene. The five Salmonella-positive samples recovered from this study, and 20 similar Salmonella-positive samples from a previous UKHSA (2020/2021) study (which had been stored frozen), were subjected to the cooking procedures described on the sample product packaging for fan assisted ovens. No Salmonella were detected in any of these 25 samples after cooking. The current survey provides evidence of the presence of Salmonella in frozen, breaded and battered chicken products in the UK food chain, although at a considerably lower incidence than reported in an earlier (2020/2021) study carried out by PHE/UKHSA as part of an outbreak investigation where Salmonella prevalence was found to be 8.8%. The current survey also provides data on the prevalence of specified AMR bacteria found in the tested chicken products on retail sale in the UK. It will contribute to monitoring trends in AMR prevalence over time within the UK, support comparisons with data from other countries, and provide a baseline against which to monitor the impact of future interventions. While AMR activity was observed in some of the E. coli and Salmonella spp. examined in this study, the risk of acquiring AMR bacteria from consumption of these processed chicken products is low if the products are cooked thoroughly and handled hygienically.
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Jorgensen, Frieda, John Rodgers, Daisy Duncan, Joanna Lawes, Charles Byrne, and Craig Swift. Levels and trends of antimicrobial resistance in Campylobacter spp. from chicken in the UK. Food Standards Agency, September 2022. http://dx.doi.org/10.46756/sci.fsa.dud728.
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Campylobacter spp. are the most common bacterial cause of foodborne illness in the UK, with chicken considered to be the most important vehicle of transmission for this organism. It is estimated there are 500,000 cases of campylobacteriosis in the UK annually, with Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli) accounting for approximately 91% and 8 % of infections, respectively. Although severe infection in humans is uncommon, treatment is seldom needed for human infection but usually involves the administration of a macrolide (e.g., azithromycin) or a fluoroquinolone (e.g., ciprofloxacin). An increased rate of resistance in Campylobacter in chicken to such antimicrobials could limit effective treatment options for human infections and it is therefore important to monitor changes in rates of resistance over time. In this report we analysed trends in antimicrobial resistance (AMR) in C. jejuni and C. coli isolated from chicken in the UK. The chicken samples were from chicken reared for meat (ie. broiler chicken as opposed to layer chicken (ie. egg-laying chicken)) and included chicken sampled at slaughterhouses as well as from retail stores in the UK. Datasets included AMR results from retail surveys of Campylobacter spp. on chicken sampled in the UK from various projects in the time period from 2001 to 2020. In the retail surveys, samples were obtained from stores including major and minor retail stores throughout the UK (in proportion to the population size of each nation) and Campylobacter spp. testing was performed using standard methods with the majority of isolates obtained from direct culture on standard media (mCCDA). Data from national scale surveys of broiler chicken, sampling caecal contents and carcase neckskins at slaughterhouses, undertaken by APHA in 2007/2008, and between 2012 and 2018 were also included in the study. In the APHA-led surveys, Campylobacter were isolated using standard culture methods (culture onto mCCDA) and antimicrobial susceptibility testing was performed by a standard microbroth dilution method to determine the minimum inhibitory concentration (MIC) of isolates. Care was taken when comparing data from different studies as there had been changes to the threshold used to determine if an isolate was susceptible or resistant to an antimicrobial in a small number of scenarios. Harmonised thresholds (using epidemiological cut-off (ECOFF) values) were employed to assess AMR with appropriate adjustments made where required to allow meaningful comparisons of resistance prevalence over time. Data from additional isolates where resistance to antimicrobials were predicted from genome sequence data were also considered.
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Weil, Clifford F., Anne B. Britt, and Avraham Levy. Nonhomologous DNA End-Joining in Plants: Genes and Mechanisms. United States Department of Agriculture, July 2001. http://dx.doi.org/10.32747/2001.7585194.bard.
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Repair of DNA breaks is an essential function in plant cells as well as a crucial step in addition of modified DNA to plant cells. In addition, our inability to introduce modified DNA to its appropriate locus in the plant genome remains an important hurdle in genetically engineering crop species.We have taken a combined forward and reverse genetics approach to examining DNA double strand break repair in plants, focusing primarily on nonhomologous DNA end-joining. The forward approach utilizes a gamma-plantlet assay (miniature plants that are metabolically active but do not undergo cell division, due to cell cycle arrest) and has resulted in identification of five Arabidopsis mutants, including a new one defective in the homolog of the yeast RAD10 gene. The reverse genetics approach has identified knockouts of the Arabidopsis homologs for Ku80, DNA ligase 4 and Rad54 (one gene in what proves to be a gene family involved in DNA repair as well as chromatin remodeling and gene silencing)). All these mutants have phenotypic defects in DNA repair but are otherwise healthy and fertile. Additional PCR based screens are in progress to find knockouts of Ku70, Rad50, and Mre11, among others. Two DNA end-joining assays have been developed to further our screens and our ability to test candidate genes. One of these involves recovering linearized plasmids that have been added to and then rejoined in plant cells; plasmids are either recovered directly or transformed into E. coli and recovered. The products recovered from various mutant lines are then compared. The other assay involves using plant transposon excision to create DNA breaks in yeast cells and then uses the yeast cell as a system to examine those genes involved in the repair and to screen plant genes that might be involved as well. This award supported three graduate students, one in Israel and two in the U.S., as well as a technician in the U.S., and is ultimately expected to result directly in five publications and one Masters thesis.
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Jorgensen, Frieda, Andre Charlett, Craig Swift, Anais Painset, and Nicolae Corcionivoschi. A survey of the levels of Campylobacter spp. contamination and prevalence of selected antimicrobial resistance determinants in fresh whole UK-produced chilled chickens at retail sale (non-major retailers). Food Standards Agency, June 2021. http://dx.doi.org/10.46756/sci.fsa.xls618.
Full textAbstract:
Campylobacter spp. are the most common bacterial cause of foodborne illness in the UK, with chicken considered to be the most important vehicle for this organism. The UK Food Standards Agency (FSA) agreed with industry to reduce Campylobacter spp. contamination in raw chicken and issued a target to reduce the prevalence of the most contaminated chickens (those with more than 1000 cfu per g chicken neck skin) to below 10 % at the end of the slaughter process, initially by 2016. To help monitor progress, a series of UK-wide surveys were undertaken to determine the levels of Campylobacter spp. on whole UK-produced, fresh chicken at retail sale in the UK. The data obtained for the first four years was reported in FSA projects FS241044 (2014/15) and FS102121 (2015 to 2018). The FSA has indicated that the retail proxy target for the percentage of highly contaminated raw whole retail chickens should be less than 7% and while continued monitoring has demonstrated a sustained decline for chickens from major retailer stores, chicken on sale in other stores have yet to meet this target. This report presents results from testing chickens from non-major retailer stores (only) in a fifth survey year from 2018 to 2019. In line with previous practise, samples were collected from stores distributed throughout the UK (in proportion to the population size of each country). Testing was performed by two laboratories - a Public Health England (PHE) laboratory or the Agri-Food & Biosciences Institute (AFBI), Belfast. Enumeration of Campylobacter spp. was performed using the ISO 10272-2 standard enumeration method applied with a detection limit of 10 colony forming units (cfu) per gram (g) of neck skin. Antimicrobial resistance (AMR) to selected antimicrobials in accordance with those advised in the EU harmonised monitoring protocol was predicted from genome sequence data in Campylobacter jejuni and Campylobacter coli isolates The percentage (10.8%) of fresh, whole chicken at retail sale in stores of smaller chains (for example, Iceland, McColl’s, Budgens, Nisa, Costcutter, One Stop), independents and butchers (collectively referred to as non-major retailer stores in this report) in the UK that are highly contaminated (at more than 1000 cfu per g) with Campylobacter spp. has decreased since the previous survey year but is still higher than that found in samples from major retailers. 8 whole fresh raw chickens from non-major retailer stores were collected from August 2018 to July 2019 (n = 1009). Campylobacter spp. were detected in 55.8% of the chicken skin samples obtained from non-major retailer shops, and 10.8% of the samples had counts above 1000 cfu per g chicken skin. Comparison among production plant approval codes showed significant differences of the percentages of chicken samples with more than 1000 cfu per g, ranging from 0% to 28.1%. The percentage of samples with more than 1000 cfu of Campylobacter spp. per g was significantly higher in the period May, June and July than in the period November to April. The percentage of highly contaminated samples was significantly higher for samples taken from larger compared to smaller chickens. There was no statistical difference in the percentage of highly contaminated samples between those obtained from chicken reared with access to range (for example, free-range and organic birds) and those reared under standard regime (for example, no access to range) but the small sample size for organic and to a lesser extent free-range chickens, may have limited the ability to detect important differences should they exist. Campylobacter species was determined for isolates from 93.4% of the positive samples. C. jejuni was isolated from the majority (72.6%) of samples while C. coli was identified in 22.1% of samples. A combination of both species was found in 5.3% of samples. C. coli was more frequently isolated from samples obtained from chicken reared with access to range in comparison to those reared as standard birds. C. jejuni was less prevalent during the summer months of June, July and August compared to the remaining months of the year. Resistance to ciprofloxacin (fluoroquinolone), erythromycin (macrolide), tetracycline, (tetracyclines), gentamicin and streptomycin (aminoglycosides) was predicted from WGS data by the detection of known antimicrobial resistance determinants. Resistance to ciprofloxacin was detected in 185 (51.7%) isolates of C. jejuni and 49 (42.1%) isolates of C. coli; while 220 (61.1%) isolates of C. jejuni and 73 (62.9%) isolates of C. coli isolates were resistant to tetracycline. Three C. coli (2.6%) but none of the C. jejuni isolates harboured 23S mutations predicting reduced susceptibility to erythromycin. Multidrug resistance (MDR), defined as harbouring genetic determinants for resistance to at least three unrelated antimicrobial classes, was found in 10 (8.6%) C. coli isolates but not in any C. jejuni isolates. Co-resistance to ciprofloxacin and erythromycin was predicted in 1.7% of C. coli isolates. 9 Overall, the percentages of isolates with genetic AMR determinants found in this study were similar to those reported in the previous survey year (August 2016 to July 2017) where testing was based on phenotypic break-point testing. Multi-drug resistance was similar to that found in the previous survey years. It is recommended that trends in AMR in Campylobacter spp. isolates from retail chickens continue to be monitored to realise any increasing resistance of concern, particulary to erythromycin (macrolide). Considering that the percentage of fresh, whole chicken from non-major retailer stores in the UK that are highly contaminated (at more than 1000 cfu per g) with Campylobacter spp. continues to be above that in samples from major retailers more action including consideration of interventions such as improved biosecurity and slaughterhouse measures is needed to achieve better control of Campylobacter spp. for this section of the industry. The FSA has indicated that the retail proxy target for the percentage of highly contaminated retail chickens should be less than 7% and while continued monitoring has demonstrated a sustained decline for chickens from major retailer stores, chicken on sale in other stores have yet to meet this target.
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Fridman, Eyal, and Eran Pichersky. Tomato Natural Insecticides: Elucidation of the Complex Pathway of Methylketone Biosynthesis. United States Department of Agriculture, December 2009. http://dx.doi.org/10.32747/2009.7696543.bard.
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Plant species synthesize a multitude of specialized compounds 10 help ward off pests. and these in turn may well serve as an alternative to synthetic pesticides to reduce environmental damage and health risks to humans. The general goal of this research was to perform a genetic and biochemical dissection of the natural-insecticides methylketone pathway that is specific to the glandular trichomes of the wild species of tomato, Solanumhabrochaites f. glabratum (accession PI126449). Previous study conducted by us have demonstrated that these compounds are synthesized de novo as a derivate pathway of the fatty acid biosynthesis, and that a key enzyme. designated MethylketoneSynthase 1 (MKS 1). catalyzes conversion of the intermediate B-ketoacyl- ACPs to the corresponding Cn-1 methylketones. The approach taken in this proposed project was to use an interspecific F2 population. derived from the cross between the cultivated lV182 and the wild species PIl26449. for three objectives: (i) Analyze the association between allelic status of candidate genes from the fatty acid biosynthesis pathway with the methylketone content in the leaves (ii) Perform bulk segregant analysis of genetic markers along the tomato genome for identifying genomic regions that harbor QTLs for 2TD content (iii) Apply differential gene expression analysis using the isolated glands of bulk segregant for identifying new genes that are involved in the pathway. The genetic mapping in the interspecific F2 population included app. 60 genetic markers, including the candidate genes from the FAS pathway and SSR markers spread evenly across the genome. This initial; screening identified 5 loci associated with MK content including the candidate genes MKS1, ACC and MaCoA:ACP trans. Interesting observation in this genetic analysis was the connection between shape and content of the glands, i.e. the globularity of the four cells, typical to the wild species. was associated with increased MK in the segregating population. In the next step of the research transcriptomic analysis of trichomes from high- and 10w-MK plants was conducted. This analysis identified a new gene, Methy1ketone synthase 2 (MKS2), whose protein product share sequence similarity to the thioesterase super family of hot-dog enzymes. Genetic analysis in the segregating population confirmed its association with MK content, as well as its overexpression in E. coli that led to formation of MK in the media. There are several conclusions drawn from this research project: (i) the genetic control of MK accumulation in the trichomes is composed of biochemical components in the FAS pathway and its vicinity (MKS 1 and MKS2). as well as genetic factors that mediate the morphology of these specialized cells. (ii) the biochemical pathway is now realized different from what was hypothesized before with MKS2 working upstream to I\1KS 1 and serves as the interface between primary (fatty acids) and secondary (MK) metabolism. We are currently testing the possible physical interactions between these two proteins in vitro after the genetic analysis showed clear epistatic interactions. (iii) the regulation of the pathway that lead to specialized metabolism in the wild species is largely mediated by transcription and one of the achievements of this project is that we were able to isolate and verify the specificity of the MKS1 promoter to the trichomes which allows manipulation of the pathways in these cells (currently in progress). The scientific implications of this research project is the advancement in our knowledge of hitherto unknown biochemical pathway in plants and new leads for studying a new family in plants (hot dog thioesterase). The agricultural and biotechnological implication are : (i) generation of new genetic markers that could assist in importing this pathway to cultivated tomato hence enhancing its natural resistance to insecticides, (ii) the discovery of MKS2 adds a new gene for genetic engineering of plants for making new fatty acid derived compounds. This could be assisted with the use of the isolated and verified MKS1 promoter. The results of this research were summarized to a manuscript that was published in Plant Physiology (cover paper). to a chapter in a proceeding book. and one patent was submitted in the US.
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Gafny, Ron, A. L. N. Rao, and Edna Tanne. Etiology of the Rugose Wood Disease of Grapevine and Molecular Study of the Associated Trichoviruses. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575269.bard.
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Rugose wood is a complex disease of grapevines, characterized by modification of the woody cylinder of affected vines. The control of rugose wood is based on the production of healthy propagation material. Detection of rugose wood in grapevines is difficult and expensive: budwood from tested plants is grafted onto sensitive Vitis indicators and the appearance of symptoms is monitored for 3 years. The etiology of rugose wood is complex and has not yet been elucidated. Several elongated clostero-like viruses are consistently found in affected vines; one of them, grapevine virus A (GVA), is closely associated with Kober stem grooving, a component of the rugose wood complex. GVA has a single-stranded RNA genome of 7349 nucleotides, excluding a polyA tail at the 3' terminus. The GVA genome includes five open reading frames (ORFs 1-5). ORF 4, which encodes for the coat protein of GVA, is the only ORF for which the function was determined experimentally. The original objectives of this research were: 1- To produce antisera to the structural and non-structural proteins of GVA and GVB and to use these antibodies to establish an effective detection method. 2- Develop full length infectious cDNA clones of GVA and GVB. 3- Study the roll of GVA and GVB in the etiology of the grapevine rugose wood disease. 4- Determine the function of Trichovirus (now called Vitivirus) encoded genes in the virus life cycle. Each of the ORFs 2, 3, 4 and 5 genes of GVA were cloned and expressed in E. coli and used to produce antisera. Both the CP (ORF 4) and the putative MP (ORF 3) were detected with their corresponding antisera in-GVA infected N. benthamiana and grapevine. The MP was first detected at an early stage of the infection, 6-12 h after inoculation, and the CP 2-3 days after inoculation. The MP could be detected in GVA-infected grapevines that tested negative for CP, both with CP antiserum and with a commercially available ELISA kit. Antisera to ORF 2 and 5 encoded proteins could react with the recombinant proteins but failed to detect both proteins in GVA infected plants. A full-length cDNA clone of grapevine virus A (GVA) was constructed downstream from the bacteriophage T7 RNA polymerase promoter. Capped in vitro transcribed RNA was infectious in N. benthamiana and N. clevelandii plants. Symptoms induced by the RNA transcripts or by the parental virus were indistinguishable. The infectivity of the in vitro-transcribed RNA was confirmed by serological detection of the virus coat and movement proteins and by observation of virions by electron microscopy. The full-length clone was modified to include a gus reporter gene and gus activity was detected in inoculated and systemic leaves of infected plants. Studies of GVA mutants suggests that the coat protein (ORF 4) is essential for cell to cell movement, the putative movement protein (ORF 3) indeed functions as a movement protein and that ORF 2 is not required for virus replication, cell to cell or systemic movement. Attempts to infect grapevines by in-vitro transcripts, by inoculation of cDNA construct in which the virus is derived by the CaMV 35S promoter or by approach grafting with infected N. benthamiana, have so far failed. Studies of the subcellular distribution of GFP fusion with each of ORF 2, 3 and 4 encoded protein showed that the CP fusion protein accumulated as a soluble cytoplasmatic protein. The ORF 2 fusion protein accumulated in cytoplasmatic aggregates. The MP-GFP fusion protein accumulated in a large number of small aggregates in the cytoplasm and could not move from cell to cell. However, in conditions that allowed movement of the fusion protein from cell to cell (expression by a PVX vector or in young immature leaves) the protein did not form cytoplasmatic aggregates but accumulated in the plasmodesmata.
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Balfanz, Emma, Erin Sandford, Michael G. Kaiser, and Susan J. Lamont. Differential Immunological Gene Expression after Escherichia coli Infection in Chickens. Ames (Iowa): Iowa State University, January 2011. http://dx.doi.org/10.31274/ans_air-180814-668.
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Goodman, E. M., and B. Greenebaum. Weak Electromagnetic Field Effects on Gene Expression in E. coli. Fort Belvoir, VA: Defense Technical Information Center, March 1996. http://dx.doi.org/10.21236/ada306447.
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