[Comparison of antibacterial effect of rifampicin and cephaloridine on a model of E. coli pyelonephritis in rats].
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Acute Disease↗
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Results for “E. coli modelling”
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New structural model of E. coli aspartate transcarbamylase and the amino-acid sequence of the regulatory polypeptide chain.
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Amino Acid Sequence↗
Antimicrobial tissue penetration in a rat model of E. coli epididymitis.
Following induction of unilateral epididymitis by intratesticular injection of E. coli, a single intraperitoneal dose of amdinocillin, ampicillin, doxycycline, tobramycin, or trimethoprim/sulfamethoxazole was administered to five groups of rats. The animal was sacrificed serially and concentrations of antibiotic in serum, infected epididymides, and non-infected epididymides were determined by high performance liquid chromatography. The ratio of infected to non-infected tissue area under the curve values was 1.05 for trimethoprim, 1.58 for sulfamethoxazole, 1.67 for amdinocillin, 2.01 for tobramycin, 2.25 for doxycycline, and 2.58 for ampicillin. Except for trimethoprim, infected tissue concentrations were significantly greater than compared to uninfected epididymal levels (p less than 0.05). Antibiotic concentrations in infected epididymides compared to serum revealed overall penetration of 34% for amdinocillin, 66% for sulfamethoxazole, 70% for ampicillin, 76% for tobramycin, 256% for trimethoprim, and 257% for doxycycline. In a rat model of epididymitis, trimethoprim and doxycycline demonstrated the greatest degree of epididymal penetration compared to serum. All antibiotics except trimethoprim had significantly greater penetration into infected tissue when compared to non-infected epididymal tissue.
Animals↗
Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase ( ubiA transferase) and characterization of potential active sites.
4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligoprenyltransferase or any structurally related enzyme is known. Knowledge of the tertiary structure and possible active sites is, however, essential for understanding the catalysis mechanism and the substrate specificity. With homology modeling techniques, secondary structure prediction tools, molecular dynamics simulations, and energy optimizations, a model with two putative active sites could be created and refined. One active site selected to be the most likely one for the docking of oligoprenyl diphosphate and 4-hydroxybenzoic acid is located near the N-terminus of the enzyme. It is widely accepted that residues forming an active site are usually evolutionary conserved within a family of enzymes. Multiple alignments of a multitude of related proteins clearly showed 100% conservation of the amino acid residues that form the first putative active site and therefore strongly support this hypothesis. However, an additional highly conserved region in the amino acid sequence of the ubiA enzyme could be detected, which also can be considered a putative (or rudimentary) active site. This site is characterized by a high sequence similarity to the aforementioned site and may give some hints regarding the evolutionary origin of the ubiA enzyme. Semiempirical quantum mechanical PM3 calculations have been performed to investigate the thermodynamics and kinetics of the catalysis mechanism. These results suggest a near S(N)1 mechanism for the cleavage of the diphosphate ion from the isoprenyl unit. The 4-hydroxybenzoic acid interestingly appears not to be activated as benzoate anion but rather as phenolate anion to allow attack of the isoprenyl cation to the phenolate, which appeared to be the rate limiting step of the whole process according to our quantum chemical calculations. Our models are a basis for developing inhibitors of this enzyme, which is crucial for bacterial aerobic metabolism. [figure: see text]. Structure of the model of ubiA oligoprenyltransferase derived from the photosynthetic reaction center (1PRC). Putative active amino acid residues and substrates are shown as capped sticks to describe their location and geometry in the putative active sites. The violet spheres identify Mg2+.
Amino Acid Sequence↗
Infant mouse model of E. coli diarrhoea: clinical protection induced by vaccination of the mothers.
Protection of infant mice against experimental E. coli B41 diarrhoea by immunization of the mothers with homologous E. coli strain was studied. The influence of the number, dose, route and moment of vaccination(s) on protection, measured by the reduced mortality rate of infant mice during the 15 days following oral challenge, was tested. The highest dose of vaccine, namely 10(8) formalin-killed E. coli by parenteral routes or 3 X 10(9) live E. coli by peroral (p.o.) route resulted in the best effect, whatever the immunization procedure used. A single vaccination of the mothers mainly delayed death without marked reduction of the mortality rate. Subcutaneous (s.c.) immunization with 10(8) formalin-killed E. coli was nevertheless more efficient than p.o. vaccination with 3 X 10(8) live E. coli. Equal levels of protection were observed when the above s.c. vaccination occurred either 15 days before the onset of gestation or on the 8th day or 15th day. In contrast, the p.o. immunization resulted in no effect when done on the 15th day of gestation. Great improvement in protection was obtained with two vaccinations, when priming occurred 15 days before the onset of gestation and boosting on the 8th day, except with two combined p.o. vaccinations with 3 X 10(8) live E. coli. Both dosages of priming and boosting seemed to matter. Peroral, subcutaneous or intraperitoneal priming with about 10(8) E. coli resulted in nearly equal effects, when boosting occurred subcutaneously with 10(8) killed E. coli. However, i.p. priming probably resulted in some non-specific effect, as shown by the slower clinical evolution of the controls. A tenfold dosage increase in p.o. priming alone led to the best protective effect observed when boosting was done three weeks after priming. The occurrence of s.c. boosting one week later, namely four weeks after priming, markedly improved protection with every route tested, and more particularly with the s.c. one. However, complete protection was never obtained. Protective effect was mostly transmitted after birth by the colostrum and the milk of the immune mothers, as demonstrated by cross-fostering experiments. Using the best immunization procedures, variability of the model was studied, by repeating experiments several times. Clinical evolution of the controls was very similar from one experiment to another, whatever the route and the moment of immunizations. In contrast, vaccinated groups showed variations which increased with time, especially on and after seven days following inoculation. Clinical evolution of individual litters belonging to the same experimental group indicated that each mother did not equally respond to the vaccination.
Animals↗
Observations on complement activity in the two-stage inflammatory/hemostatic response in the baboon and human models of E. coli sepsis and endotoxemia.
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Animals↗
[Research on lactose-splitting enzymes. XI. The reaction of 2,4-dinitrofluorobenzene with beta-galactosidase from E. coli and model experiments with insulin and ribonclease].
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Dinitrofluorobenzene↗
A modular minimal cell model: purine and pyrimidine transport and metabolism.
A more complete understanding of the relationship of cell physiology to genomic structure is desirable. Because of the intrinsic complexity of biological organisms, only the simplest cells will allow complete definition of all components and their interactions. The theoretical and experimental construction of a minimal cell has been suggested as a tool to develop such an understanding. Our ultimate goal is to convert a "coarse-grain" lumped parameter computer model of Escherichia coli into a genetically and chemically detailed model of a "minimal cell." The base E. coli model has been converted into a generalized model of a heterotrophic bacterium. This coarse-grain minimal cell model is functionally complete, with growth rate, composition, division, and changes in cell morphology as natural outputs from dynamic simulations where only the initial composition of the cell and of the medium are specified. A coarse-grain model uses pseudochemical species (or modules) that are aggregates of distinct chemical species that share similar chemistry and metabolic dynamics. This model provides a framework in which these modules can be "delumped" into chemical and genetic descriptions while maintaining connectivity to all other functional elements. Here we demonstrate that a detailed description of nucleotide precursors transport and metabolism is successfully integrated into the whole-cell model. This nucleotide submodel requires fewer (12) genes than other theoretical predictions in minimal cells. The demonstration of modularity suggests the possibility of developing modules in parallel and recombining them into a fully functional chemically and genetically detailed model of a prokaryote cell.
Adenylate Kinase↗
Non-toxigenic Escherichia coli O157:H7 strain NCTC12900 causes attaching-effacing lesions and eae-dependent persistence in weaned sheep.
Ruminants are regarded as a primary reservoir for Escherichia coli O157:H7, an important human pathogen. Intimin, encoded by the Locus of Enterocyte Effacement by E. coli O157:H7 organisms, has been cited as one bacterial mechanism of colonisation of the gastrointestinal tract. To confirm this and to test whether a non-toxigenic E. coli O157:H7 strain would colonise and persist in a sheep model, E. coli O157:H7 strain NCTC12900, that lacks Shiga toxin (stx) genes, was evaluated for use in a sheep model of persistence. Following oral inoculation of six-week-old sheep, persistent excretion of NCTC12900 was observed for up to 48 days. E. coli O157-associated attaching-effacing (AE) lesions were detected in the caecum and rectum of one six-week-old lamb, one day after inoculation. This is the first recorded observation of AE lesions in orally inoculated weaned sheep. Also, mean faecal excretion scores of NCTC12900 and an isogenic intimin (eae)-deficient mutant were determined from twenty-four six-week-old orally inoculated sheep. The eae mutant was cleared within 20 days and had lower mean excretion scores at all time points after day one post inoculation compared with the parental strain that was still being excreted at 48 days. Tissues were collected post mortem from animals selected at random from the study groups over the time course of the experiment. The eae mutant was detected in only 1/43 samples but the parental strain was recovered from 64/140 samples primarily from the large bowel although rumen, duodenum, jejunum, and ileum were culture positive especially from animals that were still excreting at and beyond 27 days after inoculation.
Adhesins, Bacterial↗
Cockayne syndrome: defective repair of transcription?
In the past years, it has become increasingly evident that basal metabolic processes within the cell are intimately linked and influenced by one another. One such link that recently has attracted much attention is the close interplay between nucleotide excision DNA repair and transcription. This is illustrated both by the preferential repair of the transcribed strand of active genes (a phenomenon known as transcription-coupled repair, TCR) as well as by the distinct dual involvement of proteins in both processes. The mechanism of TCR in eukaryotes is still largely unknown. It was first discovered in mammals by the pioneering studies of Hanawalt and colleagues, and subsequently identified in yeast and Escherichia coli. In the latter case, one protein, the transcription repair-coupling factor, was found to accomplish this function in vitro, and a plausible model for its activity was proposed. While the E. coli model still functions as a paradigm for TCR in eukaryotes, recent observations prompt us to believe that the situation in eukaryotes is much more complex, involving dual functionality of multiple proteins.
Animals↗
The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis.
The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.
Animals↗
Antibacterial activity of the bladder mucosa.
Antibacterial activity of bladder mucosa is believed to be a host defense against infection. In this study we examined the antibacterial activity of the bladder mucosa without the effect of voiding. In addition we examined whether the property of adherence was advantageous for the organism in contact with the bladder mucosa. For this, three adhering and three nonadhering strains of E. coli were placed in contact with the bladder mucosa for 4 h in an in vivo rabbit model. E. coli grown in broth and applied to 32 bladders increased in titer by 1 log. E. coli grown in rabbit urine and applied to seven bladders increased in titer by 1.2 log. In contrast E. coli inoculated into control vials containing broth increased in titer by 2.3 log (P = 0.01). There was no significant difference in the titer between adhering and nonadhering strains of E. coli after 4 h of contact with the bladder mucosa. Bladder mucosa may have an inhibitory effect on bacterial growth (regardless of adherence characteristics) and with urine flow serves to prevent infection of the bladder urine.
Adult↗
Modeling the survival of Escherichia coli O157:H7 in apple cider using probability distribution functions for quantitative risk assessment.
Outbreaks of foodborne illness from apple cider have prompted research on the survival of Escherichia coli O157:H7 in this food. Published results vary widely, potentially due to differences in E. coli O157:H7 strains, enumeration media, and other experimental considerations. We developed probability distribution functions for the change in concentration of E. coli O157:H7 (log CFU/day) in cider using data from scientific publications for use in a quantitative risk assessment. Six storage conditions (refrigeration [4 to 5 degrees C]; temperature abuse [6 to 10 degrees C]; room temperature [20 to 25 degrees C]; refrigerated with 0.1% sodium benzoate, 0.1% potassium sorbate, or both) were modeled. E. coli survival rate data for all three unpreserved cider storage conditions were highly peaked, and these data were fit to logistic distributions: ideal refrigeration, logistic (-0.061, 0.13); temperature abuse, logistic (-0.0982, 0.23); room temperature, logistic (-0.1, 0.29) and uniform (-4.3, -1.8), to model the very small chance of extremely high log CFU reductions. There were fewer published studies on refrigerated, preserved cider, and these smaller data sets were modeled with beta (4.27, 2.37) x 2.2 - 1.6, normal (-0.2, 0.13), and gamma (1.45, 0.6) distributions, respectively. Simulations were run to show the effect of storage on E. coli O157:H7 during the shelf life of apple cider. Under every storage condition, with and without preservatives, there was an overall decline in E. coli O157:H7 populations in cider, although a small fraction of the time a slight increase was seen.
Beverages↗
Sequence alignment of citrate synthase proteins using a multiple sequence alignment algorithm and multiple scoring matrices.
The alignment of Escherichia coli citrate synthase to pig heart citrate synthase and the multiple alignment of the known sequences of the citrate synthase family of enzymes have been performed using six different amino acid similarity scoring matrices and a large range of gap penalty ratios for insertions and deletions of amino acids. The alignment studies have been performed as the first step in a project aimed at homology modelling E. coli citrate synthase (a hexamer) from pig heart citrate synthase (a dimer) in a molecular modelling approach to the study of multi-subunit enzymes. The effects of several important variables in producing realistic alignments have been investigated. The difference between multiple alignment of the family of enzymes versus simple pairwise alignment of the pig heart and E. coli proteins was explored. The effects of initial separate multiple alignments of the most highly related or most homologous species of the family of enzymes upon a subsequent pairwise alignment between species was evaluated. The value of 'fingerprinting' certain residues to bias the alignment in favour of matching those residues, as well as the worth of the computerized approach compared to an intuitive alignment technique, were assessed.
Algorithms↗
Silver nanoparticles as antimicrobial agent: a case study on E. coli as a model for Gram-negative bacteria.
The antimicrobial activity of silver nanoparticles against E. coli was investigated as a model for Gram-negative bacteria. Bacteriological tests were performed in Luria-Bertani (LB) medium on solid agar plates and in liquid systems supplemented with different concentrations of nanosized silver particles. These particles were shown to be an effective bactericide. Scanning and transmission electron microscopy (SEM and TEM) were used to study the biocidal action of this nanoscale material. The results confirmed that the treated E. coli cells were damaged, showing formation of "pits" in the cell wall of the bacteria, while the silver nanoparticles were found to accumulate in the bacterial membrane. A membrane with such a morphology exhibits a significant increase in permeability, resulting in death of the cell. These nontoxic nanomaterials, which can be prepared in a simple and cost-effective manner, may be suitable for the formulation of new types of bactericidal materials.
Anti-Bacterial Agents↗
Pathophysiology of in-vitro induced filaments, spheroplasts and rod-shaped bacteria in neutropenic mice.
This study compared the in-vitro properties and in-vivo effects of Escherichia coli filaments, spheroplasts and normal cells in a murine thigh infection model. E. coli was exposed to ceftazidime, meropenem or saline to obtain filaments, spheroplasts or normal bacilli, which were then injected into neutropenic mice. After 24 h, morphology, CFUs, local and circulating endotoxin levels, cytokine levels and mortality were recorded, and correlations between bacterial and host parameters of infection were investigated. Filaments and spheroplasts contained more endotoxin/CFU than controls. Histological studies showed that morphologically altered bacteria changed into rod-shaped cells in the absence of antibiotics. Bacterial spread to the liver was significantly higher in mice challenged with rod-shaped cells, compared with antibiotic-exposed bacteria (p 0.007). Muscle endotoxin levels correlated significantly with circulating interleukin (IL)-6 and tumour necrosis factor (TNF)-alpha, and both pro-inflammatory cytokines were correlated significantly (p 0.011). Despite a tendency toward higher local and systemic concentrations of endotoxin in the filament group, inflammatory responses and survival did not differ between groups. It was concluded that morphologically altered bacteria contain more endotoxin and can regain a rod shape after withdrawal of antibiotics, while non-antibiotic-exposed bacteria show greater spread to the liver. There was a clear intra-individual relationship between local endotoxin, systemic endotoxin, TNF-alpha and IL-6 production, but these parameters did not differ among groups.
Animals↗
[Multiplicity of auto-oscillations and steady states in an open reaction catalyzed by E. coli phosphofructokinase. Quantitative model].
A quantitative mathematical model of two-substrate reaction catalized by phosphofructokinase from E. coli has been investigated. The model takes into account the tetrameric enzyme structure and resulting kinetic peculiarities of the reaction catalized, in particular, iso-and alosteric effects of ADP on enzyme activity. Fitting of the model parameters to experimental data allowed to approximate these data with good accuracy. The ranges of admitted rates of fructose-6-phosphate input and ATP regeneration at which autooscillations and multiple steady-states occur in the system have been calculated. A minimal open system with three enzymes has been proposed for experimental demonstration of the autooscillatory behaviour.
Adenosine Diphosphate↗
Increased capacity for glutathione synthesis enhances resistance to radiation in Escherichia coli: a possible model for mammalian cell protection.
A strain of Escherichia coli, enriched in its content of gamma-glutamylcysteine synthetase and glutathione synthetase activities by recombinant DNA techniques, is more resistant to the lethal effects of gamma-irradiation than is the corresponding wild strain. Although the gene-enriched strain has higher glutathione levels than the wild strain, the observed radioresistance appears to be associated with the increased capacity of the gene-enriched strain to synthesize glutathione when irradiated rather than to the cellular levels of glutathione per se. Thus, resistance was abolished in the presence of buthionine sulfoximine, a selective inactivator of gamma-glutamylcysteine synthetase that decreases glutathione synthesis but that does not act directly to lower cellular glutathione levels. Conclusions drawn from studies on this E. coli model system may have relevance to protection of mammalian cells by glutathione.
Antimetabolites↗