scholarly journals A Comparison of Methods to Measure Fitness in Escherichia coli

2015 ◽  
Author(s):  
Michael J Wiser ◽  
Richard E Lenski
Keyword(s):  
Escherichia Coli ◽  
Traditional Method ◽  
Experimental Studies ◽  
Alternative Methods ◽  
Relative Fitness ◽  
Initial Population ◽  
Common Reference ◽  
Evolution Experiment ◽  
Mean Fitness ◽  
Changes Over Time

In order to characterize the dynamics of adaptation, it is important to be able to quantify how a population's mean fitness changes over time. Such measurements are especially important in experimental studies of evolution using microbes. The Long-Term Evolution Experiment (LTEE) with Escherichia coli provides one such system in which mean fitness has been measured by competing derived and ancestral populations. The traditional method used to measure fitness in the LTEE and many similar experiments, though, is subject to a potential limitation. As the relative fitness of the two competitors diverges, the measurement error increases because the less-fit population becomes increasingly small and cannot be enumerated as precisely. Here, we present and employ two alternatives to the traditional method. One is based on reducing the fitness differential between the competitors by using a common reference competitor from an intermediate generation that has intermediate fitness; the other alternative increases the initial population size of the less-fit, ancestral competitor. We performed a total of 480 competitions to compare the statistical properties of estimates obtained using these alternative methods with those obtained using the traditional method for samples taken over 50,000 generations from one of the LTEE populations. On balance, neither alternative method yielded measurements that were more precise than the traditional method.

scholarly journals Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

2015 ◽  
Vol 282 (1821) ◽  
pp. 20152292 ◽  
Author(s):  
Richard E. Lenski ◽  
Michael J. Wiser ◽  
Noah Ribeck ◽  
Zachary D. Blount ◽  
Joshua R. Nahum ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Power Law ◽  
Hyperbolic Model ◽  
Significant Heterogeneity ◽  
Power Law Model ◽  
Constant Environment ◽  
Hard Limit ◽  
Evolution Experiment ◽  
Mean Fitness ◽  
Over Time

Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10 000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely—or at least for a long time—even in a constant environment.

scholarly journals Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

2015 ◽  
Author(s):  
Richard E Lenski ◽  
Michael J Wiser ◽  
Noah Ribeck ◽  
Zachary D Blount ◽  
Joshua R Nahum ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Power Law ◽  
Hyperbolic Model ◽  
Significant Heterogeneity ◽  
Power Law Model ◽  
Constant Environment ◽  
Hard Limit ◽  
Evolution Experiment ◽  
Mean Fitness ◽  
Over Time

Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50,000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10,000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely-or at least for a long time-even in a constant environment.

scholarly journals Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 471-479 ◽  
Author(s):  
Michael Travisano
Keyword(s):  
Escherichia Coli ◽  
Genetic Variation ◽  
Experimental Evolution ◽  
Population Genetic ◽  
Environmental Constraints ◽  
Asymmetric Pattern ◽  
Nutrient Environment ◽  
Mean Fitness ◽  
Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

scholarly journals Segregation and the Evolution of Sex Under Overdominant Selection

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1119-1128 ◽  
Author(s):  
Elie S Dolgin ◽  
Sarah P Otto
Keyword(s):  
Correlated Response ◽  
Heterozygote Advantage ◽  
Genetic Associations ◽  
Asexual Population ◽  
Modifier Locus ◽  
Sexual And Asexual Reproduction ◽  
Overdominant Selection ◽  
Mean Fitness ◽  
Changes Over Time ◽  
Inbred Populations

AbstractThe segregation of alleles disrupts genetic associations at overdominant loci, causing a sexual population to experience a lower mean fitness compared to an asexual population. To investigate whether circumstances promoting increased sex exist within a population with heterozygote advantage, a model is constructed that monitors the frequency of alleles at a modifier locus that changes the relative allocation to sexual and asexual reproduction. The frequency of these modifier alleles changes over time as a correlated response to the dynamics at a fitness locus under overdominant selection. Increased sex can be favored in partially sexual populations that inbreed to some extent. This surprising finding results from the fact that inbred populations have an excess of homozygous individuals, for whom sex is always favorable. The conditions promoting increased levels of sex depend on the selection pressure against the homozygotes, the extent of sex and inbreeding in the population, and the dominance of the invading modifier allele.

Modified Particle Swarm Optimization with Chaotic Initialization Scheme for Unconstrained Optimization Problems

Mekatronika ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 35-43
Author(s):  
K. M. Ang ◽  
Z. S. Yeap ◽  
C. E. Chow ◽  
W. Cheng ◽  
W. H. Lim
Keyword(s):  
Particle Swarm Optimization ◽  
Optimization Problems ◽  
Experimental Studies ◽  
Particle Swarm ◽  
Test Problems ◽  
Initial Population ◽  
Swarm Optimization ◽  
Modified Particle Swarm Optimization ◽  
Initialization Scheme ◽  
Chaotic Initialization

Different variants of particle swarm optimization (PSO) algorithms were introduced in recent years with various improvements to tackle different types of optimization problems more robustly. However, the conventional initialization scheme tends to generate an initial population with relatively inferior solution due to the random guess mechanism. In this paper, a PSO variant known as modified PSO with chaotic initialization scheme is introduced to solve unconstrained global optimization problems more effectively, by generating a more promising initial population. Experimental studies are conducted to assess and compare the optimization performance of the proposed algorithm with four existing well-establised PSO variants using seven test functions. The proposed algorithm is observed to outperform its competitors in solving the selected test problems.

Alternative methods to compare safety of live-attenuated respiratory Newcastle disease vaccines in young chicks

2017 ◽  
Vol 181 (9) ◽  
pp. 236-236 ◽  
Author(s):  
Aris Malo ◽  
Sjaak de Wit ◽  
Wim A J M Swart ◽  
Jane K A Cook
Keyword(s):  
Escherichia Coli ◽  
Respiratory Tract ◽  
Newcastle Disease ◽  
Subjective Assessment ◽  
Alternative Methods ◽  
Ciliated Epithelium ◽  
Organ Cultures ◽  
Initial Attempt ◽  
Development Stages ◽  
Ethical Concerns

The work reported here is an initial attempt to find an alternative method by which the safety of live-attenuated Newcastle disease virus (NDV) vaccines for the respiratory tract of young chickens can be assessed. The current recommended methods involve either the subjective assessment of respiratory signs, or raise ethical concerns, as in the case of the intracerebral pathogenicity index. The two methods considered here were the use of tracheal organ cultures to assess the level of ciliostasis which the vaccines caused to the ciliated epithelium of the trachea and the incorporation of a pathogenic strain ofEscherichia coliin the inoculum in order to induce colibacillosis. Both methods were successful in confirming the safety of the two vaccines. However, these results are only preliminary and more studies need to be performed to determine whether one or both methods have potential, either to replace the existing statutory tests, or provide a test which might be useful during the development stages of a new live-attenuated NDV vaccine.

scholarly journals Phenotypical antimicrobial resistance data of clinical and non-clinical Escherichia coli from poultry in Germany between 2014 and 2017

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243772
Author(s):  
Octavio Mesa-Varona ◽  
Heike Kaspar ◽  
Mirjam Grobbel ◽  
Bernd-Alois Tenhagen
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Clinical Isolates ◽  
Long Term Effects ◽  
Time Intervals ◽  
Explanatory Factors ◽  
Global Threat ◽  
Changes Over Time ◽  
Resistance Data

Antimicrobial resistance (AMR) is a global threat in humans and animals, and antimicrobial usage (AMU) has been identified as a main trigger of AMR. The purpose of this work was to compare data on AMR in clinical and non-clinical isolates of Escherichia coli in German broilers and turkeys between 2014 and 2017. Furthermore, we investigated AMR changes over time and the association of changes in AMU with changes in AMR. Data on clinical and non-clinical isolates together with data on therapy frequency of broilers and turkeys were collected from German monitoring systems. Logistic regression analyses were performed to assess the association between the explanatory factors (AMU, year and isolate type) and the dependent variable (AMR). In broilers, the analysis showed lower resistance proportions of clinical isolates of E. coli to ampicillin and colistin (ampicillin: Odds ratio (OR) and 95% confidence interval (CI) = 0.44 (0.3–0.64), p<0.001; colistin: OR and 95% CI = 0.75 (0.73–0.76), p<0.001) but higher proportions for cefotaxime (OR and 95% CI = 4.58 (1.56–15.1), p = 0.007). Resistance to ampicillin, gentamicin and tetracycline was less frequent in clinical isolates in turkeys (ampicillin: OR and 95% CI = 0.4 (0.29–0.53), p<0.001; gentamicin: OR and 95% CI = 0.5 (0.26–0.94), p = 0.035; tetracycline: OR and 95% CI = 0.4 (0.29–0.55), p<0.001). The analysis found decreasing associations of AMU with resistance to tetracycline in turkeys and to colistin in broilers. Year was associated with a decrease in resistance to colistin in broilers and to tetracycline in turkeys. Differences in resistance found in this study between clinical and non-clinical isolates might play an important role in resistance prevalence. This study indicated that further data analyses over longer time intervals are required to clarify the differences found between clinical and non-clinical isolates and to assess the long-term effects of changes in AMU on the prevalence of AMR.

scholarly journals Antimicrobial activity of enterocin obtained from Enterococcus durans on Shiga-like toxin-producing Escherichia coli

2019 ◽  
Vol 49 (9) ◽  
Author(s):  
Natara Favaro Tosoni ◽  
Hugo Felix Perini ◽  
Márcia Regina Terra ◽  
Marly Sayuri Katsuda ◽  
Márcia Cristina Furlaneto ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Activity ◽  
Foodborne Pathogens ◽  
Food Contamination ◽  
Alternative Methods ◽  
Cell Integrity ◽  
Enterococcus Durans ◽  
Time Points ◽  
Food Processes ◽  
Potential Use

ABSTRACT: Shiga-like toxin-producing Escherichia coli (STEC) is an important source of food contamination that presents risks to human health. Several industrial food processes eliminate this microorganism; however, these processes can alter the characteristics of the product. Alternative methods of preservation have been identified as an option to control these foodborne pathogens. The purpose of this study was to evaluate the action of bacteriocins produced by Enterococcus durans MF5 in STEC cells. Cell-free supernatant (CFS) containing enterocins from the MF5 isolate was tested over different time points (6, 18, and 24 h). Enterocins present in the crude CFS showed inhibition against STEC at all time points. In the investigation of cell integrity, using propidium iodide and fluorescence microscopy, considerable cell death was observed within 6 h of the cells being in contact with the enterocins, which was also observed at the 18 and 24 h time points. These results showed that the enterocins produced by the MF5 isolate have potential use in the control of STEC.

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