scholarly journals Short Term Evolutionary Dynamics ofEscherichia Coliin Different Carbon Environments

2018 ◽  
Author(s):  
Debika Choudhury ◽  
Supreet Saini
Keyword(s):  
Evolutionary Dynamics ◽  
Growth Dynamics ◽  
Lag Phase ◽  
Adaptation Period ◽  
Short Term ◽  
E Coli ◽  
Phenotypic Changes ◽  
Dynamical Properties ◽  
K 12 ◽  
Mg1655 Strain

AbstractStarting from a parentalE. coliK-12 MG1655 strain, we evolve cells in five different carbon environments-glucose, arabinose, xylose, rhamnose, and a mixture of these four sugars (in a predefined ratio) for approximately 2,000 generations. At the end of the adaptation period, we quantify and compare growth dynamics of the strains in a variety of environments. The evolved strains show no specialized adaptation towards growth in the carbon medium in which they were evolved. Rather, in all environments, the evolved strains exhibited a reduced lag phase and an increased growth rate. Sequencing results reveal that these dynamical properties are not introduced via mutations in the precise loci associated with utilization of the sugar in which the bacterium was evolved in. These phenotypic changes are rather likely introduced via mutationselsewhere onthe genome. Sugar systems are known to exhibit hierarchy in utilization. Evolution in a defined environment, in our experimental framework, does not alter this hierarchy.

Antibacterial Effects of Long-Chain Polyphosphates on Selected Spoilage and Pathogenic Bacteria

2008 ◽  
Vol 71 (7) ◽  
pp. 1401-1405 ◽  
Author(s):  
JEREMY A. OBRITSCH ◽  
DOJIN RYU ◽  
LUCINA E. LAMPILA ◽  
LLOYD B. BULLERMAN
Keyword(s):  
Food Industry ◽  
Pathogenic Bacteria ◽  
Antimicrobial Activities ◽  
Lag Phase ◽  
E Coli ◽  
Inhibition Of Growth ◽  
K 12 ◽  
Chain Lengths ◽  
And Staphylococcus Aureus ◽  
Long Chain

The antimicrobial activities of four long-chain food-grade polyphosphates were studied at concentrations allowed in the food industry (<5,000 ppm) in defined basal media by determining the inhibition of growth of three gram-negative and four gram-positive spoilage and pathogenic bacteria. Both generation time and lag phase of Escherichia coli K-12, E. coli O157: H7, and Salmonella Typhimurium were increased with all of the polyphosphates tested. Bacillus subtilis and Staphylococcus aureus were more sensitive to polyphosphates, but not in all cases, with multiphased growth. The growth of Lactobacillus plantarum was inhibited by polyphosphates at concentrations above 750 ppm, but the lag time of Listeria monocytogenes was shortened by the presence of polyphosphates. No single polyphosphate was maximally inhibitory against all bacteria. Polyphosphates with chain lengths of 12 to 15 were significantly different from those with chain lengths of 18 to 21 depending on the organism and concentrations of polyphosphate used. Overall, higher polyphosphate concentrations resulted in greater inhibition of bacterial growth.

scholarly journals Transcriptional Responses of Escherichia coli K-12 and O157:H7 Associated with Lettuce Leaves

2012 ◽  
Vol 78 (6) ◽  
pp. 1752-1764 ◽  
Author(s):  
Ryan C. Fink ◽  
Elaine P. Black ◽  
Zhe Hou ◽  
Masayuki Sugawara ◽  
Michael J. Sadowsky ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Leaf Surface ◽  
Short Term ◽  
Transcriptional Responses ◽  
Content Type ◽  
E Coli ◽  
Leaf Surfaces ◽  
K 12

ABSTRACTAn increasing number of outbreaks of gastroenteritis recently caused byEscherichia coliO157:H7 have been linked to the consumption of leafy green vegetables. Although it is known thatE. colisurvives and grows in the phyllosphere of lettuce plants, the molecular mechanisms by which this bacterium associates with plants are largely unknown. The goal of this study was to identifyE. coligenes relevant to its interaction, survival, or attachment to lettuce leaf surfaces, comparingE. coliK-12, a model system, andE. coliO157:H7, a pathogen associated with a large number of outbreaks. Using microarrays, we found that upon interaction with intact leaves, 10.1% and 8.7% of the 3,798 shared genes were differentially expressed in K-12 and O157:H7, respectively, whereas 3.1% changed transcript levels in both. The largest group of genes downregulated consisted of those involved in energy metabolism, includingtnaA(33-fold change), encoding a tryptophanase that converts tryptophan into indole. Genes involved in biofilm modulation (bhsAandybiM) and curli production (csgAandcsgB) were significantly upregulated inE. coliK-12 and O157:H7. BothcsgAandbhsA(ycfR) mutants were impaired in the long-term colonization of the leaf surface, but onlycsgAmutants had diminished ability in short-term attachment experiments. Our data suggested that the interaction ofE. coliK-12 and O157:H7 with undamaged lettuce leaves likely is initiated via attachment to the leaf surface using curli fibers, a downward shift in their metabolism, and the suppression of biofilm formation.

scholarly journals KatP contributes to OxyR-regulated hydrogen peroxide resistance in Escherichia coli serotype O157 : H7

Microbiology ◽  
2009 ◽  
Vol 155 (11) ◽  
pp. 3589-3598 ◽  
Author(s):  
Gaylen A. Uhlich
Keyword(s):  
Escherichia Coli ◽  
Oxidative Damage ◽  
Physiological Role ◽  
Deletion Strain ◽  
Lag Phase ◽  
Dependent Manner ◽  
E Coli ◽  
Mutant Strains ◽  
Catalase Peroxidase ◽  
K 12

Escherichia coli K-12 defends itself against peroxide-mediated oxidative damage using two catalases, KatG and KatE, and the peroxiredoxin, alkyl hydroperoxide reductase, encoded by ahpC. In E. coli O157 : H7 strain ATCC 43895 (EDL933), plasmid pO157 carries an additional catalase-peroxidase gene, katP. KatP has been shown to be a functional catalase-peroxidase. However, deletion of pO157 does not alter the peroxide resistance of strain EDL933, leaving the physiological role of katP unclear. To examine the individual roles of peroxide-resistance genes in E. coli O157 : H7, mutant strains of ATCC 43895 were constructed bearing individual deletions of katG, katE, katP and ahpC, as well as double, triple and quadruple deletions encompassing all possible gene combinations thereof. The wild-type and all 15 mutant strains were compared for differences in aerobic growth, ability to scavenge exogenous H2O2 and resistance to exogenous peroxides. Although KatG scavenged the most exogenous H2O2, KatP scavenged statistically greater amounts than either KatE or AhpC during exponential growth. However, katG and ahpC together were sufficient for full peroxide resistance in disc diffusion assays. Strains with only katG or ahpC were the only triple deletion strains with significantly shorter generation times than the quadruple deletion strain. ahpC was the only gene that could allow rapid transition from lag phase to exponential phase in a triple deletion strain. Gene expression studies revealed that katP is an OxyR-regulated gene, but its expression is suppressed in stationary phase by RpoS. These studies indicate that pO157-borne katP contributes to the complex gene network protecting strain 43895 from peroxide-mediated oxidative damage in an OxyR-dependent manner.

Predicting Pathogen Growth during Short-Term Temperature Abuse of Raw Sausage

2009 ◽  
Vol 72 (1) ◽  
pp. 75-84 ◽  
Author(s):  
STEVEN C. INGHAM ◽  
BARBARA H. INGHAM ◽  
DARAND BORNEMAN ◽  
EMILIE JAUSSAUD ◽  
ERICA L. SCHOELLER ◽  
...  
Keyword(s):  
Experimental Data ◽  
Temperature History ◽  
Lag Phase ◽  
Escherichia Coli O157 ◽  
Short Term ◽  
Phase Duration ◽  
Pork Sausage ◽  
E Coli ◽  
Further Development ◽  
And Staphylococcus Aureus

Lag-phase duration (LPD) and growth rate (GR) values were calculated from experimental data obtained using a previously described protocol (S. C. Ingham, M. A. Fanslau, G. M. Burnham, B. H. Ingham, J. P. Norback, and D. W. Schaffner, J. Food Prot. 70:1445–1456, 2007). These values were used to develop an interval accumulation-based tool designated THERM (temperature history evaluation for raw meats) for predicting growth or no growth of Salmonella serovars, Escherichia coli O157:H7, and Staphylococcus aureus in temperature-abused raw sausage. Data (time-temperature and pathogen log CFU per gram) were obtained from six inoculation experiments with Salmonella, E. coli O157:H7, and S. aureus in three raw pork sausage products stored under different temperature abuse conditions. The time-temperature history from each experiment was entered into THERM to predict pathogen growth. Predicted and experimental results were described as growth (>0.3 log increase in CFU) or no growth (≤0.3 log increase in CFU) and compared. The THERM tool accurately predicted growth or no growth for all 18 pathogen-experiment combinations. When compared with the observed changes in log CFU values for the nine pathogen-experiment combinations in which pathogens grew, the predicted changes in log CFU values were within 0.3 log CFU for three combinations, exceeded observed values by 0.4 to 1.5 log CFU in four combinations, and were 1.2 to 1.4 log CFU lower in two combinations. The THERM tool approach appears to be useful for predicting pathogen growth versus no growth in raw sausage during temperature abuse, although further development and testing are warranted.

scholarly journals Pathogenic Escherichia coli Possess Elevated Growth Rates under Exposure to Sub-Inhibitory Concentrations of Azithromycin

Antibiotics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 735
Author(s):  
Tran Tuan-Anh ◽  
Ha Thanh Tuyen ◽  
Nguyen Ngoc Minh Chau ◽  
Nguyen Duc Toan ◽  
Tran Hanh Triet ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Morphological Characteristics ◽  
Growth Dynamics ◽  
Clinical Isolates ◽  
World Health ◽  
Whole Genome ◽  
Short Term ◽  
E Coli ◽  
Short Term Exposure

Antimicrobial resistance (AMR) has been identified by the World Health Organization (WHO) as one of the ten major threats to global health. Advances in technology, including whole-genome sequencing, have provided new insights into the origin and mechanisms of AMR. However, our understanding of the short-term impact of antimicrobial pressure and resistance on the physiology of bacterial populations is limited. We aimed to investigate morphological and physiological responses of clinical isolates of E. coli under short-term exposure to key antimicrobials. We performed whole-genome sequencing on twenty-seven E. coli isolates isolated from children with sepsis to evaluate their AMR gene content. We assessed their antimicrobial susceptibility profile and measured their growth dynamics and morphological characteristics under exposure to varying concentrations of ciprofloxacin, ceftriaxone, tetracycline, gentamicin, and azithromycin. AMR was common, with all organisms resistant to at least one antimicrobial; a total of 81.5% were multi-drug-resistant (MDR). We observed an association between resistance profile and morphological characteristics of the E. coli over a three-hour exposure to antimicrobials. Growth dynamics experiments demonstrated that resistance to tetracycline promoted the growth of E. coli under antimicrobial-free conditions, while resistance to the other antimicrobials incurred a fitness cost. Notably, antimicrobial exposure heterogeneously suppressed bacterial growth, but sub-MIC concentrations of azithromycin increased the maximum growth rate of the clinical isolates. Our results outline complex interactions between organism and antimicrobials and raise clinical concerns regarding exposure of sub-MIC concentrations of specific antimicrobials.

scholarly journals CRISPR-Cas Functional Module Exchange in Escherichia coli

mBio ◽  
2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Cristóbal Almendros ◽  
Francisco J. M. Mojica ◽  
César Díez-Villaseñor ◽  
Noemí M. Guzmán ◽  
Jesús García-Martínez
Keyword(s):  
Escherichia Coli ◽  
Evolutionary Dynamics ◽  
Functional Module ◽  
Microbial Evolution ◽  
Content Type ◽  
E Coli ◽  
Genetic Elements ◽  
Insertion Elements ◽  
K 12 ◽  
A Minor

ABSTRACTClustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes constitute the CRISPR-Cas systems found in theBacteriaandArchaeadomains. At least in some strains they provide an efficient barrier against transmissible genetic elements such as plasmids and viruses. Two CRISPR-Cas systems have been identified inEscherichia coli, pertaining to subtypes I-E (cas-E genes) and I-F (cas-F genes), respectively. In order to unveil the evolutionary dynamics of such systems, we analyzed the sequence variations in the CRISPR-Cas loci of a collection of 131E. colistrains. Our results show that the strain grouping inferred from these CRISPR data slightly differs from the phylogeny of the species, suggesting the occurrence of recombinational events between CRISPR arrays. Moreover, we determined that the primarycas-E genes ofE. coliwere altogether replaced with a substantially different variant in a minor group of strains that include K-12. Insertion elements play an important role in this variability. This result underlines the interchange capacity of CRISPR-Cas constituents and hints that at least some functional aspects documented for the K-12 system may not apply to the vast majority ofE. colistrains.IMPORTANCEEscherichia coliis a model microorganism for the study of diverse aspects such as microbial evolution and is a component of the human gut flora that may have a direct impact in everyday life. This work was undertaken with the purpose of elucidating the evolutionary pathways that have led to the present situation of its significantly different CRISPR-Cas subtypes (I-E and I-F) in several strains ofE. coli. In doing so, this information offers a novel and wider understanding of the variety and relevance of these regions within the species. Therefore, this knowledge may provide clues helping researchers better understand these systems for typing purposes and make predictions of their behavior in strains that, depending on their particular genetic dotation, would result in different levels of immunity to foreign genetic elements.

scholarly journals Tailoring a Global Iron Regulon to a Uropathogen

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Rajdeep Banerjee ◽  
Erin Weisenhorn ◽  
Kevin J. Schwartz ◽  
Kevin S. Myers ◽  
Jeremy D. Glasner ◽  
...  
Keyword(s):  
Amino Acids ◽  
Urinary Tract ◽  
Amino Acid ◽  
Regulatory Network ◽  
Iron Homeostasis ◽  
Iron Limitation ◽  
Content Type ◽  
E Coli ◽  
General Stress ◽  
K 12

ABSTRACT Pathogenicity islands and plasmids bear genes for pathogenesis of various Escherichia coli pathotypes. Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here, we dissected a regulatory network directed by the conserved iron homeostasis regulator, ferric uptake regulator (Fur), in uropathogenic E. coli (UPEC) strain CFT073. Comparing anaerobic genome-scale Fur DNA binding with Fur-dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655 showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O2-dependent synthesis of the siderophore aerobactin, encoded by an operon within a pathogenicity island. Taken together, these data suggest that in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O2 to produce aerobactin. IMPORTANCE Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that pathogenic bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important in controlling growth and survival under nutrient-limiting conditions and during transitions from the nutrient-rich environment of the lower gastrointestinal (GI) tract to the more restrictive environment of the urinary tract. The coupling of the response of iron limitation to increased demand for amino acids could be a critical attribute that sets UPEC apart from other E. coli pathotypes.

scholarly journals Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Carlos-Francisco Méndez-Cruz ◽  
Antonio Blanchet ◽  
Alan Godínez ◽  
Ignacio Arroyo-Fernández ◽  
Socorro Gama-Castro ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Knowledge Extraction ◽  
Biomedical Literature ◽  
Main Role ◽  
E Coli ◽  
Bacterial Transcription ◽  
Manual Curation ◽  
New Knowledge ◽  
Serovar Typhimurium ◽  
K 12

Abstract Transcription factors (TFs) play a main role in transcriptional regulation of bacteria, as they regulate transcription of the genetic information encoded in DNA. Thus, the curation of the properties of these regulatory proteins is essential for a better understanding of transcriptional regulation. However, traditional manual curation of article collections to compile descriptions of TF properties takes significant time and effort due to the overwhelming amount of biomedical literature, which increases every day. The development of automatic approaches for knowledge extraction to assist curation is therefore critical. Here, we show an effective approach for knowledge extraction to assist curation of summaries describing bacterial TF properties based on an automatic text summarization strategy. We were able to recover automatically a median 77% of the knowledge contained in manual summaries describing properties of 177 TFs of Escherichia coli K-12 by processing 5961 scientific articles. For 71% of the TFs, our approach extracted new knowledge that can be used to expand manual descriptions. Furthermore, as we trained our predictive model with manual summaries of E. coli, we also generated summaries for 185 TFs of Salmonella enterica serovar Typhimurium from 3498 articles. According to the manual curation of 10 of these Salmonella typhimurium summaries, 96% of their sentences contained relevant knowledge. Our results demonstrate the feasibility to assist manual curation to expand manual summaries with new knowledge automatically extracted and to create new summaries of bacteria for which these curation efforts do not exist. Database URL: The automatic summaries of the TFs of E. coli and Salmonella and the automatic summarizer are available in GitHub (https://github.com/laigen-unam/tf-properties-summarizer.git).

scholarly journals Effects of Gamification on Behavioral Change in Education: A Meta-Analysis

2021 ◽  
Vol 18 (7) ◽  
pp. 3550
Author(s):  
Jihoon Kim ◽  
Darla M. Castelli
Keyword(s):  
Behavioral Change ◽  
Information Science ◽  
Meta Analysis ◽  
Learning Outcome ◽  
Random Effects Model ◽  
Educational Setting ◽  
Short Term ◽  
Analytic Review ◽  
K 12 ◽  
Academic Search

Background: Gamified reward systems, such as providing digital badges earned for specific accomplishments, are related to student engagement in educational settings. The purpose of this study was to conduct a meta-analytic review to quantify the effects of gamified interventions on student behavioral change. Methods: A meta-analysis was performed using the following databases: The Academic Search Complete, Communication & Mass Media Complete, Education Source, ERIC, Library Information Science & Technology Abstracts, and PsycINFO. Inclusion in the review required: (a) peer-reviewed conducted between 2010 and 2019, (b) experimental controlled design, (c) gamification elements, and (d) educational setting. Results: Using a random-effects model, a statistically significant (Cohen’s d (ES) = 0.48, 95% CI = 0.33, 0.62) gamification effect was evidenced by moderate and positive grand effects sizes (ES). Gamification effects were higher with adults in higher education (ES = 0.95) than K-12 students (ES = 0.92). Brief interventions delivered in days or less than 1 week were significantly more effective (ES = 1.57) than interventions lasting up to 20 weeks (ES = 0.30). Interventions incorporating gamification elements across years (ES = −0.20) was adversely associated with behavioral change. Conclusions: Findings suggest that short-term over longer-term gamified interventions might be a promising way to initiate changes in learner’s behaviors and improve learning outcome.

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