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871 results for “escherichia coli”
A library of reporters of the global regulators of gene expression of Escherichia coli
<p>The topology of the transcription factor network (TFN) of <em>E. coli</em> is far from uniform, with 22 global regulator (GR) proteins controlling one-third of all genes. So far, their production rates cannot be tracked by comparable fluorescent proteins. We developed a library of fluorescent reporters for 16 GRs. Each consists of a single-copy plasmid coding for GFP fused to the full-length copy of the native promoter. We tracked their activity in exponential and stationary growth, and under weak and strong stresses. We show that the reporters have high sensitivity and specificity to all stresses tested and detect single-cell variability in transcription rates. Given the influence of GRs on the TFN, we expect that the new library will contribute to dissecting global transcriptional stress-response programs of <em>E. coli</em>. Moreover, it can be invaluable in bio-industrial applications that tune those programs to, instead of cell growth, favor productivity while reducing energy consumption.</p>
User Guide – Dashboard on Shiga toxin-producing Escherichia coli (STEC)
<p>Frank Boelaert</p>
Data from: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli
<p>Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying <em>bla<sub>CTX-M-1</sub></em>, in mixed cultures of isogenic <em>Escherichia coli </em>strains. Secreted products of LAB decreased <em>E. coli</em> growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.</p>
Water application method influences survival or growth of Escherichia coli on bulb onions during field curing.
<p>These data are presented in figure 2, 3, 4 and 5 of the publication entitled "Water application method influences survival or growth of Escherichia coli on bulb onions during field curing" submitted to Journal of Food Protection</p> <p> </p> <p> </p> <p> </p>
Computational Data for Weaker interdomain interactions in FimH30 from multidrug-resistant Escherichia coli ST131 mediate longer lasting interactions with mannose and enhanced adhesin function
<p>Input files for the MD simulations and the resulting trajectories. A representative trajectory is provided for the R and T state of each allele. </p>
Dataset of paper "Mechanistic modelling of solar disinfection (SODIS) kinetics of Escherichia coli, enhanced with H2O2 – Part 1: The dark side of peroxide"
<p>Data of the experimental and predicted <em>E. coli </em>inactivation and H<sub>2</sub>O<sub>2</sub> profiles under dark conditions to study the effect of rising water temperature.</p>
Dataser of paper "Mechanistic modelling of solar disinfection (SODIS) kinetics of Escherichia coli, enhanced with H2O2 – Part 2: Shine on you, crazy peroxide"
<p>Data of the experimental and predicted <em>E. coli </em>inactivation and H<sub>2</sub>O<sub>2</sub> profiles under different conditions of UV radiation, water temperature and initial H<sub>2</sub>O<sub>2</sub> concentration.</p>
Single-cell phenotypic characteristics of tolerance under recurring antibiotic exposure in Escherichia coli
<p>Non-heritable drug resistance, such as tolerance and persistence towards antibiotics, is little characterized compared to genetic resistance. Tolerance and persistence allow cells to survive application of antibiotics that are bactericidal to non-tolerant cells. Non-heritable drug resistance challenges antibiotic treatment, particularly of recurrent infections, and have implications towards heritable resistance evolution. Tolerant cells have commonly been characterized as growth arrested cells prior and during antibiotic application that quickly resume growth post-application. Here, we explore characteristic of tolerant and susceptible <em>E. coli</em> single bacteria cells to different levels of recurrent antibiotic exposure and quantify their occurrence. In using a high throughput single-cell microfluidic device, we find that tolerant cells reduce their growth rate by about 50%, but contrary to previous findings do not go into growth arrest or near growth arrest. The growth reduction is induced by antibiotic exposure and not caused by a stochastic switch or predetermined state as previously described. Cells exhibiting constant intermediate growth survived best under antibiotic exposure and selection did not primarily act on fast growing cells, as expected for a β-lactam antibiotic. Control experiments on population cultures confirmed and challenged scaling of single cell findings to population level processes. Our findings suggest a prevalent type of tolerance that differs from previously described tolerance and persister characteristics. Our described characteristics and its high frequency of occurrence supports acclaims of an underappreciated role of tolerant cells towards resistance evolution.</p>
Microscopy data from: Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli
<p>Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in <em>Escherichia coli</em>. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in <em>E. coli</em> and other bacteria. Three replication restart pathways have been identified in <em>E. coli</em>: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the <em>priB</em> replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel <em>priB </em>interactions were discovered. Far fewer connections were found with the PriA/PriC or PriC/Rep pathways, suggesting a primacy role for the PriA/PriB pathway in <em>E. coli</em>. Targeted genetic and imaging-based experiments with <em>priB</em> and its genetic partners revealed significant double-strand DNA break (DSB) accumulation in strains with mutations in <em>dam</em>, <em>rep</em>, <em>rdgC</em>, <em>lexA</em>, or <em>polA</em>. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of <em>rdgC</em> or <em>lexA</em> mutations in Δ<em>priB</em> cells. Taken together, our results highlight roles for several genes in DSB homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in <em>E. coli</em>.</p>
The effect of migration and variation on populations of Escherichia coli adapting to complex fluctuating environments
<p class="MsoNormal"><span>Migration, a critical evolutionary force, can have contrasting effects on adaptation. It can aid as well as impede adaptation. The effects of migration on microbial adaptation have been studied primarily in simple constant environments. Very little is known about the effects of migration on adaptation to complex, fluctuating environments. In our study, we subjected replicate populations of <em><span>Escherichia coli</span></em>, adapting to complex and unpredictably fluctuating environments to different proportions of clonal ancestral immigrants. Contrary to the results from simple/constant environments, the presence of clonal immigrants reduced all measured proxies of fitness. However, migration from a source population with a greater variance in fitness resulted in no change in fitness w.r.t the no-migration control, except at the highest level of migration. Thus, the presence of variation in the immigrants could counter the adverse effects of migration in complex and unpredictably fluctuating environments. Our study demonstrates that the effects of migration are strongly dependent on the nature of the destination environment and the genetic makeup of immigrants. These results enhance our understanding of the influences of migrating populations, which could help better predict the consequences of migration.</span></p>
Decoding the metabolic response of Escherichia coli for sensing trace heavy metals in water
<p>As: Raman spectra from E. coli lysate sample after exposing to As in DI water</p> <p>Cr: Raman spectra from E. coli lysate sample after exposing to Cr in DI water</p> <p>As_TapWater: Raman spectra from E. coli lysate sample after exposing to As in tap water</p> <p>WasteWater_FineTune_Dataset: Raman spectra from E. coli lysate sample after exposing to As in waste water</p> <p>WasteWater 'Unknow' Dataset: Raman spectra from E. coli lysate sample after exposing to waste water</p>
INNUENDO whole genome and core genome MLST schemas and datasets for Escherichia coli
<p><strong>Dataset</strong></p> <p>As reference dataset, 2,218 public draft or complete genome assemblies and available metadata of <em>Escherichia coli</em> have been downloaded from <a href="https://enterobase.warwick.ac.uk/species/index/ecoli">EnteroBase</a> in April 2017. Genomes have been selected on the basis of the ribosomal ST (rST) classification available in <a href="https://enterobase.warwick.ac.uk/species/index/ecoli">EnteroBase</a>: from the same rST, genomes have been randomly selected and downloaded. The number of samples for each rST in the final dataset is proportional to those available in <a href="https://enterobase.warwick.ac.uk/species/index/ecoli">EnteroBase</a> in April 2017. The dataset includes also 119<em> </em>Shiga toxin-producing <em>E.coli</em> genomes assembled with<a href="https://github.com/B-UMMI/INNUca"> INNUca v3.1 </a>belonging to the INNUENDO Sequence Dataset (<a href="https://www.ebi.ac.uk/ena/data/view/PRJEB27020">PRJEB27020</a>).</p> <p>File 'Metadata/Ecoli_metadata.txt' contains metadata information for each strain including source classification, taxa of the hosts, country and year of isolation, serotype, pathotype, classical pubMLST 7 genes ST classification, assembly source/method and Enterobase barcode. </p> <p>The directory 'Genomes' contains the 119 INNUca v3.1 assemblies of the strains listed in 'Metadata/Ecoli_metadata.txt'. Enterobase assemblies can be downloaded from http://enterobase.warwick.ac.uk/species/ecoli/search_strains using 'barcode'.</p> <p><strong>Schema creation and validation</strong></p> <p>The wgMLST schema from <a href="https://enterobase.warwick.ac.uk/species/ecoli/download_data">EnteroBase</a> have been downloaded and curated using <a href="https://github.com/B-UMMI/chewBBACA/wiki/1.-Schema-Creation"><em>chewBBACA AutoAlleleCDSCuration</em></a> for removing all alleles that are not coding sequences (CDS). The quality of the remain loci have been assessed using <a href="https://github.com/B-UMMI/chewBBACA/wiki/1.-Schema-Creation"><em>chewBBACA Schema Evaluation</em></a> and loci with single alleles, those with high length variability (i.e. if more than 1 allele is outside the mode +/- 0.05 size) and those present in less than 0.5% of the <em>Escherichia</em> genomes in <a href="https://enterobase.warwick.ac.uk/species/index/ecoli">EnteroBase</a> at the date of the analysis (April 2017) have been removed. The wgMLST schema have been further curated, excluding all those loci detected as “Repeated Loci” and loci annotated as “non-informative paralogous hit (NIPH/ NIPHEM)” or “Allele Larger/ Smaller than length mode (ALM/ ASM)” by the <a href="https://github.com/B-UMMI/chewBBACA/wiki/2.-Allele-Calling"><em>chewBBACA Allele Calling</em></a> engine in more than 1% of a dataset composed by 2,337 <em>Escherichia coli</em> genomes.</p> <p>File 'Schema/Ecoli_wgMLST_7601_schema.tar.gz' contains the wgMLST schema formatted for chewBBACA and includes a total of 7,601 loci.</p> <p>File 'Schema/Ecoli_cgMLST_2360_listGenes.txt' contains the list of genes from the wgMLST schema which defines the cgMLST schema. The cgMLST schema consists of 2,360 loci and has been defined as the loci present in at least the 99% of the 2,337 <em>Escherichia coli</em> genomes. Genomes have no more than 2% of missing loci.</p> <p>File 'Allele_Profles/Ecoli_wgMLST_alleleProfiles.tsv' contains the wgMLST allelic profile of the 2,337 <em>Escherichia coli</em> genomes of the dataset. Please note that missing loci follow the annotation of chewBBACA Allele Calling software.</p> <p>File 'Allele_Profles/Ecoli_cgMLST_alleleProfiles.tsv' contains the cgMLST allelic profile of the 2,337 <em>Escherichia coli</em> genomes of the dataset. Please note that missing loci are indicated with a zero.</p> <p><strong>Additional citations</strong></p> <p>The schema are prepared to be used with <a href="https://github.com/B-UMMI/chewBBACA/wiki"><strong>chewBBACA</strong></a>. When using the schema in this repository please cite also:</p> <blockquote> <p>Silva M, Machado M, Silva D, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço J. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. 15/03/2018. M Gen 4(3): doi:10.1099/mgen.0.000166 <a href="http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166</a></p> </blockquote> <p><em>Escherichia coli</em> schema is a derivation of EnteroBase <em>E. coli</em> <a href="http://enterobase.warwick.ac.uk/">EnteroBase</a> wgMLST schema. When using the schema in this repository please cite also:</p> <blockquote> <p>Alikhan N-F, Zhou Z, Sergeant MJ, Achtman M (2018) A genomic overview of the population structure of <em>Salmonella</em>. PLoS Genet 14 (4):e1007261. <a href="https://doi.org/10.1371/journal.pgen.1007261">https://doi.org/10.1371/journal.pgen.1007261</a></p> </blockquote>
Supporting data and code for: Longitudinal Study on Shiga Toxin–producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk
<p>Supporting data and code for the article: "Longitudinal Study on Shiga Toxin–producing <em>Escherichia coli</em> and <em>Campylobacter jejuni</em> on Finnish Dairy Farms and in Raw Milk".</p>
Data set "Correlation of in vitro biofilm formation capacity with persistence of antibiotic-resistant Escherichia coli on fresh leafy produce"
<p>This repository contains the metadata and raw data for the analysis of an <em>in vitro </em>screening of 174 antibiotic-resistance E. coli strains isolated from various sources to evaluate their ability and strength to form biofilms.</p> <p>This repository contains the raw data to characterise a subset of eleven <em>E. coli </em>strains in their population dynamics and persistance on lamb's lettuce (<em>Valerianella locusta</em>) leaves.</p> <p>Raw images (czi format) of live/dead stain of selected strains in <em>V. locusta </em>leaves are provided.</p> <p>Data analysis and image processing scripts can be found in the GitHub repository associated to the manuscript.</p>
The role of the essential GTPase ObgE in regulating lipopolysaccharide synthesis in Escherichia coli
<p>Source data accompanying scientific publication.</p> <p>Abstract: <span>During growth, cells need to synthesize and expand their envelope, a process that requires careful regulation. Here, we show that the GTPase ObgE of <em>E. coli</em> contributes to the regulation of lipopolysaccharide (LPS) synthesis, an essential component of the Gram-negative outer membrane. Using a dominant-negative mutant (named ‘ObgE*’), we show a direct interaction between ObgE and LpxA, which catalyzes the first step in LPS synthesis. This interaction is enhanced by the mutation in ObgE* which, when bound to GTP, leads to inhibition of LpxA, decreased LPS synthesis, and cell death. Although wild-type ObgE does not exert the same strong effects as ObgE* on LpxA or LPS synthesis, our data indicate that ObgE participates in the regulation of cell envelope synthesis in <em>E. coli</em>. Because ObgE also influences other cellular functions (i.e., ribosome assembly, DNA replication, etc.), it seems increasingly plausible that this GTPase coordinates several processes to finetune cell growth.</span></p>
Dataset - Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections
<p>Dataset for manuscript posted at biorxiv: https://doi.org/10.1101/2021.01.03.42483 and in revision for eLife. Data corresponding to each main figure and its associated figure supplements are in seperate .zip folders.</p>
Морфологические трансформации (сферические формы палочковидных клеток) у фенотипов VBNC Escherichia coli и Salmonella Typhimurium в биопленочной популяции
<p>Обнаруженные морфологические трансформации (сферические формы палочковидных клеток) у фенотипов VBNC <em>Escherichia coli</em> (Б) и <em>Salmonella </em>Typhimurium (Г) в биопленочной популяции в сравнении с вегетативными аналогами – соответственно, А и В; при сохраненной целостности мембран (трансмиссионная электронная микроскопия, фото любезно предоставлены д.б.н., проф. Рыбальченко О.В.)</p>
Hypermutator emergence in experimental Escherichia coli populations is stress type dependent
<p class="Textbody"><span>Genotypes exhibiting an increased mutation rate, called hypermutators, can propagate in microbial populations because they can have an advantage due to the higher supply of beneficial mutations needed for adaptation. Although this is a frequently observed phenomenon in natural and laboratory populations, little is known about the influence of parameters such as the degree of maladaptation, stress intensity and the genetic architecture for adaptation on the emergence of hypermutators. To address this knowledge gap, we measured the emergence of hypermutators over ~1000 generations in experimental <em>Escherichia coli</em> populations exposed to different levels of osmotic or antibiotic stress. Our stress types were chosen based on the assumption that the genetic architecture for adaptation differs between them. Indeed, we show that the size of the genetic basis for adaptation is larger for osmotic stress compared to antibiotic stress. During our experiment, we observed an increased emergence of hypermutators in populations exposed to osmotic stress but not in those exposed to antibiotic stress, indicating that hypermutator emergence rates are stress-type-dependent. These results support our hypothesis that hypermutator emergence is linked to the size of the genetic basis for adaptation. In addition, we identified other parameters that covaried with stress type (stress level and IS transposition rates) that might have contributed to an increased hypermutator provision and selection. Our results provide a first comparison of hypermutator emergence rates under varying stress conditions and point towards complex interactions of multiple stress-related factors on the evolution of mutation rates.</span></p>
Data from: Phenotypic plasticity of antibiotic resistance, metabolism byproduct utilization and the evolution of mutually beneficial cooperation in Escherichia coli
<p><span>Although tag-based donation and recognition have well explained how the cooperative individuals are positively assorted if the cooperative individuals possess some signals and are also able to detect such signals, an additional mechanism is required to explain why some individuals pay the costs of evolving such a tag that may not be rewarded subsequently, and how such tag-based cooperative individuals will meet other similar individuals with a very low mutation rate. Here, we show that many and even all<em> Escherichia coli </em>bacteria cells in the increased antibiotic concentration will plastically evolve to be antibiotic resistant individuals who could protect antibiotic sensitive strain from the attack of antibiotics, and the antibiotic resistant strain could reversibly evolve to be antibiotic sensitive in non-antibiotic supplement medium but in a harsher environment with low glucose. A further experiment showed that antibiotic-sensitive <em>E. coli </em>strain could in turn help reduce the concentration of indole produced by the resistant strain. This metabolic product is harmful to the growth of the antibiotic-resistant strain but benefits the antibiotic-sensitive strain by helping turn on the multi-drug exporter to discharge the antibiotic. The utilization of metabolism byproduct indole produced by antibiotic-resistant cells benefits antibiotic-sensitive cells, while the indole-absorbing service of antibiotic sensitive cells unconsciously help in nullifying the indole side effect on antibiotic resistant strain, and a mutual benefit cooperation could therefore evolve.</span></p>
Data from: Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli
<p>The evolution of a novel trait can profoundly change an organism's effects on its environment, which can in turn affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following the evolution of a novel function in the Long-Term Evolution Experiment (LTEE) with <em>Escherichia</em> <em>coli</em>. A characteristic feature of <em>E. coli</em> is its inability to grow aerobically on citrate (Cit<sup>−</sup>). Nonetheless, a Cit<sup>+</sup> variant with this capacity evolved in one LTEE population after 31,000 generations. The Cit<sup>+</sup>clade then coexisted stably with another clade that retained the ancestral Cit<sup>−</sup> phenotype. This coexistence was shaped by the evolution of a cross-feeding relationship based on C<sub>4</sub>-dicarboxylic acids, particularly succinate, fumarate, and malate, that the Cit<sup>+</sup> variants release into the medium. Both the Cit<sup>−</sup> and Cit<sup>+</sup> cells evolved to grow on these excreted resources. The evolution of aerobic growth on citrate thus led to a transition from an ecosystem based on a single limiting resource, glucose, to one with at least five resources that were either shared or partitioned between the two coexisting clades. Our findings show that evolutionary novelties can change environmental conditions in ways that facilitate diversity by altering ecosystem structure and the evolutionary trajectories of coexisting lineages.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.