scholarly journals Elementary growth modes/vectors and minimal autocatalytic sets for kinetic/constraint-based models of cellular growth

2021 ◽  
Author(s):  
Stefan Müller
Keyword(s):  
Growth Rate ◽  
Maximum Growth ◽  
Linear Constraints ◽  
Maximum Growth Rate ◽  
Cellular Growth ◽  
Metabolic Pathway Analysis ◽  
Elementary Flux Modes ◽  
Autocatalytic Sets ◽  
Growth Modes ◽  
Cellular Phenotypes

AbstractElementary vectors are fundamental objects in polyhedral geometry. In metabolic pathway analysis, elementary vectors range from elementary flux modes (of the flux cone) and elementary flux vectors (of a flux polyhedron) via elementary conversion modes (of the conversion cone) to minimal cut sets (of a dual polyhedron) in computational strain design.To better understand cellular phenotypes with optimal (or suboptimal) growth rate, we introduce and analyze classes of elementary vectors for models of cellular growth. Growth modes (GMs) only depend on stoichiometry, but not on growth rate or concentrations; they are elements of the growth cone. Elementary growth modes (EGMs) are conformally nondecomposable GMs; unlike elementary flux modes, they are not support-minimal, in general. Most importantly, every GM can be written as a conformal sum of EGMs. Growth vectors (GVs) and elementary growth vectors (EGVs) also depend on growth rate, concentrations, and linear constraints; they are elements of a growth polyhedron. Again, every GV can be written as a conformal sum of EGVs. To relate the new concepts to other branches of theory, we define autocatalytic GMs and the corresponding (minimal) autocatalytic sets of reactions.As a case study, we consider whole cell models (simple kinetic models of self-fabrication). First, we use EGMs to derive an upper bound for growth rate that only depends on enzyme kinetics. Next, we study growth rate maximization (via control parameters for ribosome kinetics). In particular, we analyze growth states (GSs) and elementary growth states (EGSs) as introduced in [de Groot et al, 2020]. Unlike EGMs, EGSs depend on (metabolite) concentrations and growth rate. Most importantly, (i) we show that EGSs are support-minimal, (ii) we give a simple proof for the fact that maximum growth rate is attained at an EGS, and (iii) we show that, at every optimal EGS, the ribosome capacity constraint is active. Finally, we determine the dependence of EGSs on growth rate, and we study the relation between EGSs and minimal autocatalytic sets, EGMs, and elementary flux modes. Along the way, we point out (and resolve) mathematical issues in [de Groot et al, 2020].

scholarly journals Elementary vectors and autocatalytic sets for computational models of cellular growth

2021 ◽  
Author(s):  
Stefan Müller ◽  
Diana Széliová ◽  
Jürgen Zanghellini
Keyword(s):  
Growth Rate ◽  
Computational Models ◽  
Lipid Synthesis ◽  
Cellular Growth ◽  
Ammonium Uptake ◽  
Biomass Composition ◽  
Elementary Flux Modes ◽  
Autocatalytic Sets ◽  
Growth Modes ◽  
Cellular Phenotypes

Traditional models of cellular growth involve an approximative biomass ''reaction'' which specifies biomass composition in terms of precursor metabolites (such as amino acids and nucleotides). On the one hand, biomass composition is often not known exactly and may vary drastically between extreme conditions; on the other hand, the predictions of computational models crucially depend on biomass. Even elementary flux modes (EFMs) depend on the biomass reaction. (To be specific: not just the numerical values of the EFMs, but also their supports and their number.) To better understand cellular phenotypes across conditions, we introduce and analyze new classes of elementary vectors for more comprehensive models of cellular growth, involving explicit synthesis reactions for all macromolecules. Growth modes (GMs) are given by stoichiometry, and elementary growth modes (EGMs) are GMs that cannot be decomposed without cancellations. Unlike EFMs, EGMs need not be support-minimal. Most importantly, every GM can be written as a sum of EGMs. In models with additional (capacity) constraints, growth vectors (GVs) and elementary growth vectors (EGVs) also depend on growth rate. In any case, EGMs/EGVs do not depend on the biomass composition. In fact, they cover all possible biomass compositions and can be seen as unbiased versions of elementary flux modes/vectors (EFMs/EFVs) used in traditional models. To relate the new concepts to other branches of theory, we define autocatalytic GMs and the corresponding autocatalytic sets of reactions. Further, we illustrate our results in a small model of a self-fabricating cell, involving glucose and ammonium uptake, amino acid and lipid synthesis, and the expression of all enzymes and the ribosome itself. In particular, we study the variation of biomass composition as a function of growth rate. In agreement with experimental data, low nitrogen uptake correlates with high carbon (lipid) storage.

A note on growth curves of rabbit lines selected on growth rate or litter size

1993 ◽  
Vol 57 (2) ◽  
pp. 332-334 ◽  
Author(s):  
A. Blasco ◽  
E. Gómez
Keyword(s):  
Growth Rate ◽  
Litter Size ◽  
Growth Curves ◽  
Live Weight ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Standard Errors ◽  
Adult Weight ◽  
Weight Growth ◽  
Using Data

Two synthetic lines of rabbits were used in the experiment. Line V, selected on litter size, and line R, selected on growth rate. Ninety-six animals were randomly collected from 48 litters, taking a male and a female each time. Richards and Gompertz growth curves were fitted. Sexual dimorphism appeared in the line V but not in the R. Values for b and k were similar in all curves. Maximum growth rate took place in weeks 7 to 8. A break due to weaning could be observed in weeks 4 to 5. Although there is a remarkable similarity of the values of all the parameters using data from the first 20 weeks only, the higher standard errors on adult weight would make 30 weeks the preferable time to take data for live-weight growth curves.

Reassessment of Maximum Growth Rates for C3 and C4 Crops

1978 ◽  
Vol 14 (1) ◽  
pp. 1-5 ◽  
Author(s):  
J. L. Monteith
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Growing Season ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Crop Growth ◽  
Close Inspection ◽  
Similar Difference ◽  
Photosynthetic Efficiencies

SUMMARYFigures for maximum crop growth rates, reviewed by Gifford (1974), suggest that the productivity of C3 and C4 species is almost indistinguishable. However, close inspection of these figures at source and correspondence with several authors revealed a number of errors. When all unreliable figures were discarded, the maximum growth rate for C3 stands fell in the range 34–39 g m−2 d−1 compared with 50–54 g m−2 d−1 for C4 stands. Maximum growth rates averaged over the whole growing season showed a similar difference: 13 g m−2 d−1 for C3 and 22 g m−2 d−1 for C4. These figures correspond to photosynthetic efficiencies of approximately 1·4 and 2·0%.

Interpretation of Experimental Data with Regard to the Activated Sludge Model No.1 and Calibration of the Model for Municipal Wastewater Treatment Plants

1992 ◽  
Vol 25 (6) ◽  
pp. 167-183 ◽  
Author(s):  
H. Siegrist ◽  
M. Tschui
Keyword(s):  
Experimental Data ◽  
Growth Rate ◽  
Activated Sludge ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Municipal Wastewater Treatment ◽  
Activated Sludge Model

The wastewater of the municipal treatment plants Zürich-Werdhölzli (350000 population equivalents), Zürich-Glatt (110000), and Wattwil (20000) have been characterized with regard to the activated sludge model Nr.1 of the IAWPRC task group. Zürich-Glatt and Wattwil are partly nitrifying treatment plants and Zürich-Werdhölzli is fully nitrifying. The mixing characteristics of the aeration tanks at Werdhölzli and Glatt were determined with sodium bromide as a tracer. The experimental data were used to calibrate hydrolysis, heterotrophic growth and nitrification. Problems arising by calibrating hydrolysis of the paniculate material and by measuring oxygen consumption of heterotrophic and nitrifying microorganisms are discussed. For hydrolysis the experimental data indicate first-order kinetics. For nitrification a maximum growth rate of 0.40±0.07 d−1, corresponding to an observed growth rate of 0.26±0.04 d−1 was calculated at 10°C. The half velocity constant found for 12 and 20°C was 2 mg NH4-N/l. The calibrated model was verified with experimental dam of me Zürich-Werdhölzli treatment plant during ammonia shock load.

Dietary Protein Requirements of Fishes — A Reassessment

1987 ◽  
Vol 44 (11) ◽  
pp. 1995-2001 ◽  
Author(s):  
Stephen H. Bowen
Keyword(s):  
Growth Rate ◽  
Dietary Protein ◽  
Protein Concentration ◽  
Trophic Ecology ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Intake Rate ◽  
Protein Requirement ◽  
Fish Physiology ◽  
Protein Retention

It is widely believed that fishes require more dietary protein than other vertebrates. Many aspects of fish physiology, nutrition, and trophic ecology have been interpreted within the context of this high protein requirement. Here, fishes are compared with terrestrial homeotherms in terms of (1) protein requirement for maintenance, (2) relative protein concentration in the diet required for maximum growth rate, (3) protein intake rate required for maximum growth rate, (4) efficiency of protein retention in growth, and (5) weight of growth achieved per weight of protein ingested. The two animal groups compared differ only in relative protein concentration in the diet required for maximum growth rate. This difference is explained in terms of homeotherms' greater requirement for energy and does not reflect absolute differences in protein requirement. The remaining measures of protein requirement suggest that fishes and terrestrial homeotherms are remarkably similar in their use of protein as a nutritional resource. Reinterpretation of the role of protein in fish physiology, nutrition, and trophic ecology is perhaps in order.

Allometric scaling and taxonomic variation in nutrient utilization traits and maximum growth rate of phytoplankton

2012 ◽  
Vol 57 (2) ◽  
pp. 554-566 ◽  
Author(s):  
Kyle F. Edwards ◽  
Mridul K. Thomas ◽  
Christopher A. Klausmeier ◽  
Elena Litchman
Keyword(s):  
Growth Rate ◽  
Allometric Scaling ◽  
Maximum Growth ◽  
Nutrient Utilization ◽  
Maximum Growth Rate

Instability waves on the air–sea interface

1993 ◽  
Vol 248 ◽  
pp. 363-381 ◽  
Author(s):  
G. H. Wheless ◽  
G. T. Csanady
Keyword(s):  
Surface Tension ◽  
Growth Rate ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Surface Velocity ◽  
Instability Waves ◽  
Interface Surface ◽  
Fluid Properties ◽  
Compound Matrix Method ◽  
Order Of Magnitude

We used a compound matrix method to integrate the Orr–Sommerfeld equation in an investigation of short instability waves (λ < 6 cm) on the coupled shear flow at the air–sea interface under suddenly imposed wind (a gust model). The method is robust and fast, so that the effects of external variables on growth rate could easily be explored. As expected from past theoretical studies, the growth rate proved sensitive to air and water viscosity, and to the curvature of the air velocity profile very close to the interface. Surface tension had less influence, growth rate increasing somewhat with decreasing surface tension. Maximum growth rate and minimum wave speed nearly coincided for some combinations of fluid properties, but not for others.The most important new finding is that, contrary to some past order of magnitude estimates made on theoretical grounds, the eigenfunctions at these short wavelengths are confined to a distance of the order of the viscous wave boundary-layer thickness from the interface. Correspondingly, the perturbation vorticity is high, the streamwise surface velocity perturbation in typical cases being five times the orbital velocity of free waves on an undisturbed water surface. The instability waves should therefore be thought of as fundamentally different flow structures from free waves: given their high vorticity, they are akin to incipient turbulent eddies. They may also be expected to break at a much lower steepness than free waves.

scholarly journals Economics Research Output in BRICS Countries: A Scientometric Dimension

2019 ◽  
Vol 9 (1) ◽  
pp. 14-21
Author(s):  
Kiran P. Savanur
Keyword(s):  
Growth Rate ◽  
Web Of Science ◽  
Research Output ◽  
Activity Index ◽  
Citation Impact ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Economic Research ◽  
Brics Countries ◽  
Economics Research

This article examines the research output of economics published by BRICS countries during 1991-2016. Data collected from the Web of Science database. Growth rate (CAGR), Collaboration index, Transformative Activity index (TAI), Co-authorship index and Relative Citation Impact (RCI) indicators have been adopted to analyze the quantity and impact of economic research. We found that all five BRICS countries contributed approximately 10 percentile of the world’s economics research. The highest contribution was made by China with a total of 4424 articles which is 40.59 percent. Russia has the maximum growth rate of 27.99. Overall collaboration rate of economics publications of BRICS countries is moderate.

scholarly journals Efficacy of Experimental Mouth Rinses on Caries-Related Biofilms in vitro

2021 ◽  
Vol 2 ◽  
Author(s):  
Josiana Steiger ◽  
Olivier Braissant ◽  
Tuomas Waltimo ◽  
Monika Astasov-Frauenhoffer
Keyword(s):  
Growth Rate ◽  
Antimicrobial Agents ◽  
Growth Parameters ◽  
Screening Method ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Screening Process ◽  
Mouth Rinses ◽  
Amine Fluoride

This study assessed the efficacy of tin and Polyethylenglycol (PEG-3) tallow aminopropylamine in different concentrations on Streptococcus mutans (S. mutans) biofilms to establish a new screening process for different antimicrobial agents and to gain more information on the antibacterial effects of these agents on cariogenic biofilms. Isothermal microcalorimetry (IMC) was used to determine differences in two growth parameters: lag time and growth rate; additionally, reduction in active biofilms was calculated. Experimental mouth rinses with 400 and 800 ppm tin derived from stannous fluoride (SnF2) revealed results (43.4 and 49.9% active biofilm reduction, respectively) similar to meridol mouth rinse (400 ppm tin combined with 1,567 ppm PEG-3 tallow aminopropylamine; 55.3% active biofilm reduction) (p &gt; 0.05), while no growth of S. mutans biofilms was detected during 72 h for samples treated with an experimental rinse containing 1,600 ppm tin (100% active biofilm reduction). Only the highest concentration (12,536 ppm) of rinses containing PEG-3 tallow aminopropylamine derived from amine fluoride (AmF) revealed comparable results to meridol (57.5% reduction in active biofilm). Lower concentrations of PEG-3 tallow aminopropylamine showed reductions of 16.9% for 3,134 ppm and 33.5% for 6,268 ppm. Maximum growth rate was significantly lower for all the samples containing SnF2 than for the samples containing control biofilms (p &lt; 0.05); no differences were found between the control and all the PEG-3 tallow aminopropylamine (p &gt; 0.05). The growth parameters showed high reproducibility rates within the treated groups of biofilms and for the controls; thus, the screening method provided reliable results.

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