Modeling bacterial growth responses

Summary The main steps of modeling bacterial growth responses are summarized and a new model for growth curves is shown. Its advantages are analyzed from some theoretical and practical points of view. The new model fits better and has more advantageous statistical properties than the Gompertz curve.     

Simulated tissue growth for 3D printed scaffolds

Experiments have demonstrated biological tissues grow by mechanically sensing their localized curvature, therefore making geometry a key consideration for tissue scaffold design. We developed a simulation approach for modeling tissue growth on beam-based geometries of repeating unit cells, with four lattice topologies considered. In simulations, tissue was seeded on surfaces with new tissue growing in empty voxels with positive curvature. Growth was fastest on topologies with more beams per unit cell when unit cell volume/porosity was fixed, but fastest for topologies with fewer beams per unit cell when beam width/porosity was fixed. Tissue filled proportional to mean positive surface curvature per volume. Faster filling scaffolds had lower permeability, which is important to support nutrient transport, and highlights a need for tuning geometries appropriately for conflicting trade-offs. A balance among trade-offs was found for scaffolds with beam diameters of about \(300\,\upmu \hbox {m}\) and 50% porosity, therefore providing the opportunity for further optimization based on criteria such as mechanical factors. Overall, these findings provide insight into how curvature-based tissue growth progresses in complex scaffold geometries, and a foundation for developing optimized scaffolds for clinical applications.     

Modelling the bacterial growth/no growth interface

A logistic regression model is proposed which enables one to model the boundary between growth and no growth for bacterial strains in the presence of one or more growth controlling factors such as temperature, pH and additives such as salt and sodium nitrite. The form of the expression containing the growth limiting factors may be suggested by a kinetic model, while the response at a given combination of factors may either be presence/absence (i.e. growth/no growth) or probabilistic (i.e. r successes in n trials). The approach described represents an integration of the probability and kinetic aspects of predictive microbiology, and a unification of predictive microbiology and the hurdle concept. The model is illustrated using data for Shigella flexneri.     

Phospholipid metabolism during bacterial growth

Haemophilus parainfluenzae incorporates glycerol and phosphate into the membrane phospholipids without lag during logarithmic growth. In phosphatidyl glycerol (PG), the phosphate and unacylated glycerol moieties turn over and incorporate radioactivity much more rapidly than does the diacylated glycerol. At least half the radioactivity is lost from the phosphate and unacylated glycerol in about 1 doubling. The total fatty acids turn over slightly faster than the diacyl glycerol. In phosphatidyl ethanolamine (PE), which is the major lipid of the bacterium, ethanolamine and phosphate turn over and incorporate radioactivity at least half as fast as the phosphate in PG. The glycerol of PE did not turn over in 4 bacterial doublings. In phosphatidic acid the glycerol turns over at one-third the rate of phosphate turnover. By means of a modified method for the quantitative recovery of 1,3-glycerol diphosphate from cardiolipin, the phosphates and middle glycerol of cardiolipin were shown to turn over more rapidly than the acylated glycerols during bacterial growth. There is no randomization of the radioactivity in the 1- and 3-positions of the glycerol in the course of 1 doubling. The fatty acids of PG turn over faster than those in PE. In both lipids the 2-fatty acids turn over much faster than the 1-fatty acids. At both positions the individual fatty acids have their own rates of turnover. The distribution of fatty acids between the 1- and 2-positions is the same as in other organisms, with more monoenoic and long-chain fatty acids at the 2-position. The different rates of turnover and incorporation of radioactivity into different parts of the lipids suggest that exchange reactions may be important to phospholipid metabolism.     

Monod's bacterial growth model revisited

An attempt to justify Monod's bacterial growth model is presented. The justification is based on a mechanistic approach to growth which leads to a differential equation with delay and then to Monod's model. An unexpected increase of parameterK _s with μ_m is predicted by the theory. A survey of literature shows that this effect is present in a large majority of published data.     

Trait-based approach to bacterial growth efficiency

Bacterial growth efficiency (BGE) is the proportion of assimilated carbon that is converted into biomass and reflects the balance between growth and energetic demands. Often measured as an aggregate property of the community, BGE is highly variable within and across ecosystems. To understand this variation, we first identified how species identity and resource type affect BGE using 20 bacterial isolates belonging to the phylum Proteobacteria that were enriched from north temperate lakes. Using a trait-based approach that incorporated genomic and phenotypic information, we characterized the metabolism of each isolate and tested for predicted trade-offs between growth rate and efficiency. A substantial amount of variation in BGE could be explained at broad (i.e., order, 20%) and fine (i.e., strain, 58%) taxonomic levels. While resource type was a relatively weak predictor across species, it explained >60% of the variation in BGE within a given species. A metabolic trade-off (between maximum growth rate and efficiency) and genomic features revealed that BGE may be a species-specific metabolic property. Our study suggests that genomic and phylogenetic information may help predict aggregate microbial community functions like BGE and the fate of carbon in ecosystems.     

Soil minerals affect taxon-specific bacterial growth

Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages—particularly short-range order minerals—affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with ¹⁸O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25–36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.Subject terms: Biogeochemistry, Microbial ecology, Biogeochemistry     

细菌生长的热谱图测定

The fundamental growth thermograms of bacteria have been determined by using the microcalorimetric method. These perfect thermogram curves reflect the changes of bacterial growth patterns (including the lag phase of growth, log growth, stationary phase and the decline phase of growth). In our experiments, highly characteristic and reproducible growth patterns are observed under the same condition, therefore one can use these thermograms as "finger print" to discriminate bacteria. On the other hand, there thermogram curves contain ample information, which are very significant for the studies on microorganism metabolism, bio-thermokinetic and clinical fields.     

Simulated brain tumor growth dynamics using a three-dimensional cellular automaton

We have developed a novel and versatile three-dimensional cellular automaton model of brain tumor growth. We show that macroscopic tumor behavior can be realistically modeled using microscopic parameters. Using only four parameters, this model simulates Gompertzian growth for a tumor growing over nearly three orders of magnitude in radius. It also predicts the composition and dynamics of the tumor at selected time points in agreement with medical literature. We also demonstrate the flexibility of the model by showing the emergence, and eventual dominance, of a second tumor clone with a different genotype. The model incorporates several important and novel features, both in the rules governing the model and in the underlying structure of the model. Among these are a new definition of how to model proliferative and non-proliferative cells, an isotropic lattice, and an adaptive grid lattice.     

Tracking bacterial growth in liquid media and a new bacterial life model

By increasing viscosity of liquid media above 8.4 centipoise (cp) i.e. 0.084 g·cm~(-1)·S~(-1) individual growth and family formation of Escherichia coli was continuously observed in real-time for up to 6 h. The observations showed primarily unidirectional growth and reproduction of E. coli and suggested more than one reproduction in the observed portion of E. coli life span. A new bacterial life model is proposed: each bacterium has a stable cell polarity that ultimately transforms into two bacteria of different generations; the life cycle of a bacterium can contain more than one reproduction cycle; and the age of a bacterium should be defined by its experienced chronological time. This new bacterial life model differs from the dominant concepts of bacterial life but complies with all basic life principles based on direct observation of macroorganisms.     

Tracking bacterial growth in liquid media and a new bacterial life model

By increasing viscosity of liquid media above 8.4 centipoise (cp) i.e. 0.084 g· cm^-1 · s^-1, individual growth and family formation ofEscherichia coli was continuously observed in real-time for up to 6 h. The observations showed primarily unidirectional growth and reproduction ofE. coli and suggested more than one reproduction in the observed portion ofE. coli life span. A new bacterial life model is proposed: each bacterium has a stable cell polarity that ultimately transforms into two bacteria of different generations; the life cycle of a bacterium can contain more than one reproduction cycle; and the age of a bacterium should be defined by its experienced chronological time. This new bacterial life model differs from the dominant concepts of bacterial life but complies with all basic life principles based on direct observation of macroorganisms.