Thesis. 1976. M.S.--Massachusetts Institute of Technology. Dept. of Civil Engineering. / Microfiche copy available in Archives and Engineering. / Bibliography: leaves 63-64. / M.S.

L'objet de cette thèse est la formulation et l'étude de modèles structurés de croissance dans un chemostat, qui est un appareil permettant la culture de micro-organismes dans des conditions très contrôlées. Plus particulièrement, nous serons intéressés par la description de la taille d'organismes phytoplanctoniques. Dans une première partie, nous donnons quelques précisions biologiques, présentons ensuite le dispositif expérimental, puis introduisons les modèles élémentaires utilisés pour la description mathématique du chemostat. La deuxième et principale partie de cette thèse commence par une introduction aux modèles structurés de populations, l'accent étant mis sur la description des populations cellulaires. Ensuite sont étudiés successivement des modèles discrets en temps détaillant de manière précise la division cellulaire, des modèles en équations différentielles ordinaires vérifiant la propriété dite de conservation de la matière, et enfin une classe de modèles ne vérifiant pas cette propriété. Nous terminons cette thèse par une ouverture sur les possibles applications à d'autres contextes du type de modélisation que nous développons.

In vitro gut models provide several advantages over in vivo models for the study of the human gut microbiota. However, because communities developed in these models are simplified simulations of the in vivo environment it is necessary to characterize the reproducibility, repeatability and stability of cultured communities. We also need to broadly define the differences between in vitro consortia and the communities from which they are derived. In this study we characterized and validated a twin-vessel (independent, identical) single-stage chemostat model of the human distal gut. Samples were analyzed using a molecular fingerprinting technique (Denaturing Gradient Gel Electrophoresis) to compare and monitor changes in the overall structure of the communities while a phylogenetic microarray (Human Intestinal Tract Chip) was used to obtain phylogenetic information. We found that twin-vessels inoculated with feces developed and maintained diverse communities that reached stable compositions by at most 36 days post-inoculation. Communities were enriched in Bacteroidetes but not Clostridium cluster XIVa, Bacilli or other Firmicutes relative to the fecal inocula. Vessels were very reproducible when inoculated with identical fecal inocula, less similar when inoculated with consecutive fecal donations from the same donor, and maintained donor-specific identities when inoculated with feces from different donors. Norepinephrine exposure (undefined perturbation) did not appear to have a substantial effect on the structure of chemostat communities, while clindamycin treatment (defined perturbation) caused large changes in the structure of chemostat communities. Packed-column biofilm reactors incorporated a simulated mucosal environment into our chemostat system, allowing us to simultaneously culture biologically relevant planktonic and biofilm communities that were complex, reproducible, and distinct. Defined communities were comparable to fecal communities at the phylum/class-level but established stable compositions more rapidly. While it was difficult to assess the persistence of synthetic stool in a healthy fecal chemostat community (+/- antibiotic perturbation), mixing communities from two donors resulted in a mixed community that more closely resembled one donor over the other. Although future experimentation is required, the results presented here show our twin-vessel single-stage chemostat model represents a valid simulation of the human distal gut environment and can support complex, representative microbial communities ideal for experimental manipulation. / Canadian Institutes of Health Research; Ontario Ministry of Agriculture, Food and Rural Affairs; Ontario Ministry of Research and Innovation; Canada Foundation for Innovation; Ontario Ministry of Training, Colleges and Universities

Thesis (M. S.)--Civil and Environmental Engineering, Georgia Institute of Technology, 2006. / Dr. Kurt Pennell, Committee Member; Dr. Jim Spain, Committee Member; Dr. Joseph Hughes, Committee Chair

Fitness, the competitive advantage of an organism or gene, is the basis for adaptation and the emergence of complexity in biology. Competitive advantage is contextual, as it is affected by environmental pressures and ecological interactions. To enable experiments with complex environmental dynamics, we developed eVOLVER, a novel platform for scalable programmable continuous culture. In this thesis, we apply eVOLVER to interrogate how competitive outcomes between strains change according to environmental conditions. Using soil microbe communities as a model ecological system, we tuned dilution rate and frequency across 112 cultures in eVOLVER and observed replicable changes in composition and diversity. Our experimental results challenge intuition about the relationship between diversity and disturbance. In collaborative work, we compared different models of competitive growth in simulations. A Monod growth model outperforms Lotka-Volterra and linear consumer resource models at predicting the effect of varying dilution profiles on microbial diversity. We hypothesize that trade-offs in growth rate and nutritional requirements (r/K) create distinct niches which permit coexistence at certain mortality rates, but collapse under others. These findings suggest a mechanism that potentially affects diversity-disturbance relationships, and confirm that temporal fluctuations can promote diversity. In separate studies, we apply these methods and concepts to 1) study selection on a genome-scale library in yeast under conditions of fluctuating temperature stress in eVOLVER and 2) evaluate the persistence of engineered microbial spores relative to native strains in different “real-world” environments (e.g. soil) and perturbations. Broadly, this dissertation demonstrates that the combination of next-generation sequencing and scalable programmable culture technologies finally enables the types of experiments needed to test decades of theoretical work in ecology and evolution. / 2021-05-18T00:00:00Z

No description available.

Introduction: Clostridium thermocellum is considered a model organism forconsolidated bioprocessing, due to its ability to hydrolyze lignocellulosicbiomass more efficiently than many other organisms and to produce ethanol.In order to meet the industrial requirements of ethanol yield and titer, metabolicengineering efforts have been made resulting in a strain that successfullydisplays increased ethanol yield with reduced amount of some byproducts.However, the ethanol yield in this engineered strain still does not meet theindustrial requirements and significant amounts of amino acids are stillproduced. To attempt to decrease the level of amino acid excretion intended toimprove the ethanol yield in C. thermocellum, it is essential to understand itsmetabolism and how it is affected by different cultivation conditions and mediumcompositions. This study aimed to gain an insight in how carbon- and nitrogenlimitation affect amino acid excretion in C. thermocellum, with the hypothesisthat excess of carbon and nitrogen yields more amino acid excretion. Methods: Mass-balance based calculations of rates and yields were used toanalyze the metabolism of a wild-type of C. thermocellum (DSM 1313) grownanaerobically in carbon- or nitrogen-limiting chemostats. For this, Low-Carbonmedium containing, respectively, cellobiose (5 g/L) and urea (0.15 g/L) as thelimiting nutrient was used. Both cultivations were performed at 55 °C, pH 7.0and 400 RPM shaking at a dilution rate of 0.1 h-1. Conclusion:  Considering yields of total amino acids excreted in bothlimitations, it was hypothesized that C. thermocellum exploited the amino acidexcretion to maintain carbon balance around the pyruvate node caused byexcess of the carbon. Based on yield of valine excreted in particular, it washypothesized that amino acid excretion was used to maintain redox balance inthe metabolism of C. thermocellum, where malate shunt could play a major role.However, results of the Carbon-limitation did not allow any conclusion ofnitrogen excess having an effect on amino acid excretion in C. thermocellum.

Rich dynamics have been demonstrated when a discrete time delay is introduced in a simple predator-prey system. For example, Hopf bifurcations and a sequence of period doubling bifurcations that appear to lead to chaotic dynamics have been observed. In this thesis we consider two different predator-prey models: the classical Gause-type predator-prey model and the chemostat predator-prey model. In both cases, we explore how different ways of modeling the time between the first contact of the predator with the prey and its eventual conversion to predator biomass affects the possible range of dynamics predicted by the models. The models we explore are systems of integro-differential equations with delay kernels from various distributions including the gamma distribution of different orders, the uniform distribution, and the Dirac delta distribution. We study the models using bifurcation theory taking the mean delay as the main bifurcation parameter. We use both an analytical approach and a computational approach using the numerical continuation software XPPAUT and DDE-BIFTOOL. First, general results common to all the models are established. Then, the differences due to the selection of particular delay kernels are considered. In particular, the differences in regions of stability of the coexistence equilibrium are investigated. Finally, the effects on the predicted range of dynamics between the classical Gause-type and the chemostat predator-prey models are compared. / Thesis / Doctor of Philosophy (PhD)

A scarcity of comparable research on the transport of bacteria has forced hydrologic models to assume that bacteria travel as dissolved chemicals. In reality, most bacteria preferentially attach to soil aggregates, and behave very differently from planktonic bacteria. The goal of this research project was to identify and evaluate a laboratory method for partitioning between attached and planktonic bacteria that could be used to improve hydrologic modeling. Attachment was measured indirectly as the difference between total and planktonic bacterial concentration. Planktonic concentration was defined as the concentration of bacteria that could pass through an 8 μm screen. Total concentration was determined by disaggregating attached bacteria through a dispersion treatment. A randomized complete block design was structured to test for the effects of filtering, two dispersion treatment options, and the presence of soil on concentration. Tween-85 surfactant was selected as the best dispersant for use in further studies. About 78% of bovine <I>E. coli</I> in the laboratory samples were adsorbed/associated with sterile soil particles. Twenty samples of different bacteria-soil ratios were analyzed using this method to develop an isotherm equation describing <I>E. coli</I> partitioning. The <I>E. coli</I> used to inoculate these samples was cultured using a chemostat reactor to control cell growth stage and control variability. A linear isotherm (R²=0.88) was selected to describe this experimental data; however, future studies characterizing the partitioning behavior of <I>E. coli</I> under different environmental conditions are recommended in order to better understand attachment prior to modeling attached and planktonic <I>E. coli</I> separately. / Master of Science

Cette thèse s'adresse au problèmes relié au modélisation mathématique en culture continue et culture batch. Nous proposons et étudions, dans une première étape, des modèles mathématiques de quelques processus biologique en culture continue (Chemostat) permettant d'expliquer et de prévoir la coexistence et la coexistence pratique. Dans une deuxième étape, une série d'expériences de laboratoire sont munies en culture batch, et un modèle mathématique tenant compte du recyclage de substrat est proposé, analysé et validé sur des donnés expérimentales en culture pure et mixte prouvant la validité de la principe d'exclusion compétitive en culture batch. / Cette thèse s'adresse au problèmes relié au modélisation mathématique en culture continue et culture batch. Nous proposons et étudions, dans une première étape, des modèles mathématiques de quelques processus biologique en culture continue (Chemostat) permettant d'expliquer et de prévoir la coexistence et la coexistence pratique. Dans une deuxième étape, une série d'expériences de laboratoire sont munies en culture batch, et un modèle mathématique tenant compte du recyclage de substrat est proposé, analysé et validé sur des donnés expérimentales en culture pure et mixte prouvant la validité de la principe d'exclusion compétitive en culture batch.