scholarly journals A decay effect of the bacterial growth rate associated with genome reduction

2018 ◽  
Author(s):  
Kouhei Tsuchiya ◽  
Yang-Yang Cao ◽  
Masaomi Kurokawa ◽  
Kazuha Ashino ◽  
Tetsuya Yomo ◽  
...  
Keyword(s):  
Growth Rate ◽  
Decay Rate ◽  
Bacterial Growth ◽  
Growth Rates ◽  
Logistic Model ◽  
Growth Dynamics ◽  
Genome Reduction ◽  
Population Increase ◽  
Optical Turbidity ◽  
Decay Effect

AbstractBacterial growth is an important topic in microbiology and of crucial importance to better understand living cells. Bacterial growth dynamics are quantitatively examined using various methods to determine the physical, chemical or biological features of growing populations. Due to methodological differences, the exponential growth rate, which is a parameter that is representative of growth dynamics, should be differentiated. This study experimentally verified the differentiation in growth rates attributed to different methodologies, and demonstrated that the most popular method, optical turbidity, led to the determination of a lower growth rate in comparison to the methods based on colony formation and ATP abundance, due to a decay effect of reading OD600 during a population increase. Accordingly, the logistic model, which is often applied to growth data reading the OD600, was revised by introducing a new parameter: the decay rate, to compensate for the lowered estimation in growth rates. The modified logistic model not only presented an improved goodness of fit in comparison to the original model but also led to an intriguing finding of a correlation between genome reduction and the decay rate. The decay effect seemed to be partially attributed to the decrease in cell size accompanied by a population increase and was medium dependent. In summary, the present study provides not only a better theoretical tool for the high-throughput studies on bacterial growth dynamics linking with experimental data using optical turbidity to the theoretical analysis with biological importance, but also a valuable insight for understanding the genome evolution and fitness increase in microbial life.

scholarly journals Estimates of population growth rates of humpback whales (Megaptera novaeangliae) in the wintering grounds off the coast of Brazil (Breeding Stock A)

2020 ◽  
pp. 145-149
Author(s):  
Eric Ward ◽  
Alexandre N. Zerbini ◽  
Paul G. Kinas ◽  
Marcia H. Engel ◽  
Artur Andriolo
Keyword(s):  
Growth Rate ◽  
Population Growth ◽  
Growth Rates ◽  
Negative Binomial ◽  
Selection Criterion ◽  
Strong Support ◽  
Humpback Whales ◽  
Population Increase ◽  
Eastern Coast ◽  
Linear Predictor

Humpback whales wintering off the eastern coast of Brazil were heavily exploited by commercial whaling in the Southern Hemisphere. During recent years, clear signs of recovery have been observed, but few estimates of population growth rate exist. In this study, quantitative estimates of rates of population increase are obtained from sighting per unit of effort data (1995–98) using generalised linear models and maximum likelihood estimation. The error distributions considered for the models were Poisson and negative binomial. Predictors of the number of sightings included the year, month and 2-week periods during which the sightings were made. Predictors were treated as factors or numeric variables. For the numeric variables, quadratic dependence was also considered for each predictor to allow for possible non-linear relationships. Using Akaike Information Criterion (AICc) as a model selection criterion, the best model included year and month as continuous predictors. The data indicated strong support for the negative binomial over the Poisson models, but did not support models based on a finer temporal scale than month. Assuming year to be a linear predictor, the best estimate of the growth rate for the population wintering off Brazil was 7.4% per year (95% CI = 0.6–14.5%) during the period 1995–98. This estimate provides additional quantitative evidence that this population has been increasing and is consistent with the observed growth rates of other humpback whale stocks.

scholarly journals Estimation of annual compound growth rates of guava (Psidium guajava L.) fruit in Haryana using Non linear model

2019 ◽  
Vol 11 (4) ◽  
pp. 778-784
Author(s):  
Pardeep Panghal ◽  
Manoj Kumar ◽  
Sarita Rani
Keyword(s):  
Growth Rate ◽  
Linear Model ◽  
Growth Rates ◽  
Logistic Model ◽  
Linear Models ◽  
Psidium Guajava ◽  
Annual Growth Rate ◽  
Guava Fruit ◽  
Non Linear ◽  
Best Fit

Computation of growth rates plays an important role in agricultural and economic research to study growth pattern of a various commodities. Many of the research workers used the parametric approach for computation of annual growth rate but not use the concept of non-linear model.  In this paper, an attempt has been made to study growth rates of guava for three districts (Hisar, and Kurukshetra) and Haryana state as a whole using different non-linear models. The time series data on annual area and production of guava (Psidium guajava L.) in different districts of Haryana from 1990-91 to 2015-16 were collected to fit non linear models. Growth rates were computed through best fitted non-linear models. It was found that Logistic model could be best fit for computation of growth rates of area for guava fruit in Hisar and Kurukshetra district and Haryana state as a whole whereas Gompertz model was best fit for Yamunanagar district based on high R2 and least MSE and RMSE values. It was also observed that monomolecular model was best fit for production of guava fruits in Hisar and Yamunanagar district whereas Logistic model was best fit for production of guava fruit in Kurukshetra and Haryana state as a whole because of high R2 and least MSE and RMSE values. R and excel software have been used for fitting the non linear model and computation of growth rates for area and production of guava fruit for the year 1990-91 to 2015-16. None has been used the non linear model growth model for computation of annual growth rate of guava fruit for area and production of Haryana state. But in this work non linear growth model has been used for computation of growth rate instead of parametric approaches.

Experimental Sensitivity Analysis and the Equivalence of Pulsed Forcing and Feedback Control in Thermoacoustic Systems

2017 ◽  
Author(s):  
Nicholas P. Jamieson ◽  
Matthew P. Juniper
Keyword(s):  
Growth Rate ◽  
Sensitivity Analysis ◽  
Feedback Control ◽  
Decay Rate ◽  
Efficient Method ◽  
Growth Rates ◽  
Decay Rates ◽  
Control Devices ◽  
Set Up ◽  
Linear Decay

We examine the shifts in linear decay rates and growth rates, with and without control devices on a simple thermoacoustic system. When the system is stable, we measure the decay rate by pulsing with a loudspeaker. This improves on the experimental techniques developed by Rigas et al. (J. Fluid Mech., 2016, vol. 787, R1 [1]) and Jamieson et al. (Int. J. Spray and Comb. Dyn., accepted, 2016 [2]), to develop a more efficient method of experimental sensitivity analysis to apply in thermoacoustic systems. When the system is unstable, we use feedback control to bring it to a non-oscillating state. We then switch off the feedback control and measure the growth rate. The results suggest that both methods are suitable for use in the experimental sensitivity analysis of thermoacoustic systems. Our experimental set up is automated and we find that we can obtain thousands of decay rates in 1/12 the time compared with the previous work.

scholarly journals Effect of Turmeric Concentrations on the Rate of Growth of Oral Bacteria—An In-Vitro Study

2021 ◽  
Vol 9 (3) ◽  
pp. 26
Author(s):  
Yun Xuan Yang ◽  
Vicky Wu ◽  
Hadi Malak ◽  
Aliya Peer Ahamed ◽  
Aaron Lo ◽  
...  
Keyword(s):  
Growth Rate ◽  
Bacterial Growth ◽  
Growth Rates ◽  
Dental Students ◽  
Oral Bacteria ◽  
Growth Data ◽  
Bacterial Growth Rate ◽  
Bacterial Cultures ◽  
Significant Difference

Background and Aim: The aim of this study was to evaluate the effect of varying concentrations of a turmeric solution on the growth rates of oral bacteria sampled from dental students. Methods: Bacterial cultures were grown overnight in aerobic conditions from plaque samples obtained from five test subjects. With the exception of the control, samples were exposed to different treatments; including chlorhexidine gluconate 2 mg/mL, prepared turmeric solution (TS) mouthwash: TS 0.25 mL (7.375 mg/mL), TS 0.5 mL (14.75 mg/mL), and TS 1 mL (29.50 mg/mL). Growth rate of the bacterial cultures were assessed by monitoring changes in optical density readings at 600 nm at hourly intervals for a six-hour period. The data were plotted and the exponential trend was used to calculate individual rates of growth. Data was analyzed using a one-way ANOVA with the significance confirmed using the Tukey-HSD test. Results: Growth observed in the bacteria exposed to the turmeric solution, was significantly greater (p < 0.05) when compared with the bacteria exposed to the medium alone. There was a significant difference found between the bacterial growth rate of the 1 mL turmeric solution against the growth rate of the bacteria in the 0.25 and 0.5 mL turmeric solutions. Conclusion: Comparison of growth rates of oral bacteria suggested that turmeric solutions of concentrations between 7.357 and 29.5 mg/mL (0.25–1 mL) were unlikely to exhibit bacteriostatic or bactericidal properties, and, conversely, increased bacterial growth. Considering this result, it is unlikely that turmeric mouthwash made from store-bought turmeric would have any antibacterial effects against oral bacteria, and may even promote bacterial growth.

scholarly journals Comparative activity of Ceftriaxone, Ciprofloxacin and Gentamicin as a function of bacterial growth rate probed by Escherichia coli chromosome replication in the mouse peritonitis model

2018 ◽  
Author(s):  
Maria Schei Haugan ◽  
Anders Løbner-Olesen ◽  
Niels Frimodt-Møller
Keyword(s):  
Growth Rate ◽  
Bacterial Growth ◽  
Growth Dynamics ◽  
Chromosome Replication ◽  
Bacterial Cells ◽  
Bacterial Growth Rate ◽  
Pre Treatment

AbstractCommonly used antibiotics exert their effect predominantly on rapidly growing bacterial cells, yet growth dynamics taking place during infection in a complex host environment remain largely unknown. Hence, means to measure in situ bacterial growth rate is essential to predict the outcome of antibacterial treatment. We have recently validated chromosome replication as readout for in situ bacterial growth rate during Escherichia coli infection in the mouse peritonitis model. By the use of two complementary methods (qPCR and fluorescence microscopy) for differential genome origin and terminus copy number quantification, we demonstrated the ability to track bacterial growth rate, both on a population average and on a single-cell level; from one single biological specimen. Here, we asked whether the in situ growth rate could predict antibiotic treatment effect during infection in the same model. Parallel in vitro growth experiments were conducted as proof-of-concept. Our data demonstrate that the activity of commonly used antibiotics Ceftriaxone and Gentamicin correlated with pre-treatment bacterial growth rate; both drugs performing better during rapid growth than during slow growth. Conversely, Ciprofloxacin was less sensitive to bacterial growth rate, both in a homogenous in vitro bacterial population and in a more heterogeneous in vivo bacterial population. The method serves as a platform to test any antibiotic’s dependency upon active in situ bacterial growth. Improved insight into this relationship in vivo could ultimately prove helpful in evaluating future antibacterial strategies.ImportanceMost antibiotics in clinical use exert their effect predominantly on rapidly growing bacterial cells, yet there is a lack of insight into bacterial growth dynamics taking place during infection in vivo. We have applied inexpensive and easily accessible methods for extraction of in situ bacterial growth rate from bacterial chromosome replication during experimental murine infection. This approach not only allows for a better understanding of bacterial growth dynamics taking place during the course of infection, but also serves as a platform to test the activity of different antibiotics as a function of pre-treatment in situ growth rate. The method has the advantage that bacterial growth rate can be probed from a single biological sample, with the potential for extension into clinical use in pre-treatment infected biological specimens. A better understanding of commonly used antibiotics’ level of dependency upon bacterial growth, combined with measurements of in situ bacterial growth rate in infected clinical specimens, could prove helpful in evaluating future antibacterial treatment regimens.

scholarly journals A decay effect of the growth rate associated with genome reduction in Escherichia coli

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Kouhei Tsuchiya ◽  
Yang-Yang Cao ◽  
Masaomi Kurokawa ◽  
Kazuha Ashino ◽  
Tetsuya Yomo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Genome Reduction ◽  
Decay Effect

scholarly journals The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Motoki Nagai ◽  
Masaomi Kurokawa ◽  
Bei-Wen Ying
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Bacterial Growth ◽  
Bacterial Population ◽  
Growth Dynamics ◽  
Culture Conditions ◽  
Bacterial Growth Rate ◽  
Global Pattern ◽  
Microbial Genomes ◽  
Chromosomal Distance

Abstract The growth rate, representing the fitness of a bacterial population, is determined by the transcriptome. Chromosomal periodicity, which is known as the periodic spatial pattern of a preferred chromosomal distance in microbial genomes, is a representative overall feature of the transcriptome; however, whether and how it is associated with the bacterial growth rate are unknown. To address these questions, we analysed a total of 213 transcriptomes of multiple Escherichia coli strains growing in an assortment of culture conditions varying in terms of temperature, nutrition level and osmotic pressure. Intriguingly, Fourier transform analyses of the transcriptome identified a common chromosomal periodicity of transcriptomes, which was independent of the variation in genomes and environments. In addition, fitting of the data to a theoretical model, we found that the amplitudes of the periodic transcriptomes were significantly correlated with the growth rates. These results indicated that the amplitude of periodic transcriptomes is a parameter representing the global pattern of gene expression in correlation with the bacterial growth rate. Thus, our study provides a novel parameter for evaluating the adaptiveness of a growing bacterial population and quantitatively predicting the growth dynamics according to the global expression pattern.

scholarly journals The common chromosomal periodicity of transcriptomes is correlated with the bacterial growth rate

2020 ◽  
Author(s):  
Motoki Nagai ◽  
Masaomi Kurokawa ◽  
Bei-Wen Ying
Keyword(s):  
Gene Expression ◽  
Growth Rate ◽  
Bacterial Growth ◽  
Bacterial Population ◽  
Gene Expression Pattern ◽  
Growth Dynamics ◽  
Bacterial Growth Rate ◽  
Global Pattern ◽  
Global Parameter ◽  
Whole Transcriptome

AbstractThe growth rate, representing the fitness of a bacterial population, is determined by the whole transcriptome. Chromosomal periodicity is a representative overall feature of the whole transcriptome; however, whether and how it is associated with the bacterial growth rate are unknown. To address these questions, we analyzed a total of 213 transcriptomes of genetically differentiated Escherichia coli strains growing in an assortment of culture conditions varying in terms of temperature, nutrition level and osmotic pressure. Intriguingly, the Fourier transform identified a common chromosomal periodicity of transcriptomes, which was independent of the variation in genomes and environments. In addition, fitting of the theoretical model found that the amplitudes of the periodic transcriptomes were significantly correlated with the growth rates. This novel finding successfully identified a single parameter representing the global pattern of the whole transcriptome for the first time and indicated that bacterial growth was correlated with the magnitude of chromosomal differentiation in gene expression. These results provided an alternative global parameter for evaluating the adaptiveness of a growing bacterial population and provided a quantitative rule that makes it possible to predict the growth dynamics according to the gene expression pattern.

The Age Structure and Growth Dynamics of Young-Of-The-Year Bass, Dicentrarchus Labrax, Populations

1991 ◽  
Vol 71 (4) ◽  
pp. 799-810 ◽  
Author(s):  
S. Jennings ◽  
J. E. Lancaster ◽  
J. S. Ryland ◽  
S. E. Shackley
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Dicentrarchus Labrax ◽  
Growth Dynamics ◽  
Frequency Distributions ◽  
South Wales ◽  
Nursery Habitats ◽  
The Mean ◽  
Young Of The Year ◽  
Time Of Year

Back-calculated egg fertilization (spawned) dates and growth rates for young-of-the-year bass, Dicentrarchus labrax (L), captured from Loughor Estuary, Oxwich Bay and Ogmore Estuary, south Wales, UK, during 1988 and 1989 were compared. Spawned date frequency distributions indicated that the bass spawning season began in late February and continued until early June in 1988 and early July in 1989.There were no significant differences in the frequency distributions of back-calculated spawned dates for the bass populations, between either sites or years, which suggested that any variations in growth rates were attributable to characteristics of their respective environments. Growth rates were determined for bass cohorts resulting from early, midor late-season spawnings at Oxwich and Loughor in 1988 and Oxwich, Loughor and Ogmore in 1989. There were only slight intra-annual differences between the mean growth rates of bass cohorts at the same site, suggesting that bass from early cohorts would be larger at any given time of year. In 1989, growth was considerably faster at Oxwich and Loughor than at Ogmore, where food supply was considered limiting. However, between-site variations in growth rate were small in comparison with inter-annual differences. The faster growth rates observed at Loughor and Oxwich in 1989 were attributed to higher water temperatures.Relationships between growth rate and subsequent survival of young-of-the-year bass, and the relative importance of estuaries as nursery habitats for juvenile bass, are discussed.

Burst size of bacteriophage SP82 as a function of growth rate of its host Bacillus subtilis

1982 ◽  
Vol 28 (11) ◽  
pp. 1277-1280 ◽  
Author(s):  
Vera Webb ◽  
Eugene Leduc ◽  
George B. Spiegelman
Keyword(s):  
Growth Rate ◽  
Bacillus Subtilis ◽  
Cell Growth ◽  
Bacterial Growth ◽  
Growth Rates ◽  
Burst Size ◽  
Cell Growth Rate ◽  
Natural Logarithm ◽  
Bacterial Growth Rates

The burst size of bacteriophage SP82 in Bacillus subtilis has been measured under conditions of varying bacterial growth rates. The natural logarithm of the burst size was found to vary linearly with cell growth rate.

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