To see the other types of publications on this topic, follow the link: Chemostat.
Dissertations / Theses on the topic 'Chemostat'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Chemostat.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Arkin, Sinan Sadi. "Microbial evolution in the chemostat." Thesis, Imperial College London, 2010. http://hdl.handle.net/10044/1/11305.
Full text
2
Toth, Damon. "Analysis of age-structured chemostat models /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/6780.
Full text
3
Robledo, Gonzalo. "Quelques résultats sur la commande du chemostat." Phd thesis, Université de Nice Sophia-Antipolis, 2006. http://tel.archives-ouvertes.fr/tel-00069800.
Full textAbstract:
Cette thèse s'attache à la commande de certains systèmes écologiques en chemostat (appareil de culture de micro--organismes en laboratoire). Nous commençons par un aperçu des modèles de compétition et de chaîne trophique dans le chemostat ainsi qu'un rappel des concepts basiques de la théorie de la commande adaptée aux équations du chemostat. Ceci nous permet de montrer quelques applications pratiques et aussi de mettre en évidence la complexité mathématique de la commande.La première partie considère la commande robuste d'un chemostat simple qui présente des imprécisions déterministes tant dans le modèle que dans la sortie, ainsi que des retards dans la sortie. Nous construisons une famille de boucles de rétroaction qui stabilise le modèle dans un polytope déterminé
par la grandeur des imprécisions. Cette famille stabilise aussi la sortie autour d'une consigne en présence des retards, mais en l'absence d'imprécision
sur le modèle et la sortie.
La deuxième partie considère la commande en boucle
fermée d'un modèle de compétition entre espèces
qui permet la coexistence de celles--ci. Nous généralisons un résultat proposé par P. De Leenher et H.Smith dans deux directions: considération de fonctions de croissance plus générales et prise en compte de la mortalité des espèces.
La troisième partie considère la commande en boucle ouverte d'une chaîne trophique dans un chemostat. Nous présentons une méthode de réduction de dimension qui permet de caractériser l'ensemble d'atteignabilité du système et d'obtenir un
résultat sur la commandabilité partielle de la chaîne.
4
Thörngren, Sebastian. "An Multivariable Approach for the Chemostat Model." Thesis, Linnéuniversitetet, Institutionen för matematik (MA), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-48654.
Full textAbstract:
We use a multivariable approach to study the Chemostat model for a food chain. Using a Lyapunov function we reduce the system to a two-dimensional system.We then find isoclines and equilibrium points using a change of variables and the implicit function theorem.It turn out to be three equilibriums, namely the extinction equilibrium, caring capacity equilibrium and the implicit representation of an isocline where all solutions for the interior equilibrium is expressed.
5
El, Moustaid Fadoua. "MATHEMATICAL MODELING OF CYANOBACTERIAL DYNAMICS IN A CHEMOSTAT." Master's thesis, Temple University Libraries, 2015. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/335727.
Full textAbstract:
MathematicsM.S.
We present a mathematical model that describes how cyanobacterial communities use natural light as a source of energy and water as a source of electrons to perform photosynthesis and therefore, grow and co-survive together with other bacterial species. We apply our model to a phototrophic population of bacteria, namely, cyanobacteria. Our model involves the use of light as a source of energy and inorganic carbon as a source of nutrients. First, we study a single species model involving only cyanobacteria, then we include heterotrophs in the two species model. The model consists of ordinary differential equations describing bacteria and chemicals evolution in time. Stability analysis results show that adding heterotrophs to a population of cyanobacteria increases the level of inorganic carbon in the medium, which in turns allows cyanobacteria to perform more photosynthesis. This increase of cyanobacterial biomass agrees with experimental data obtained by collaborators at the Center for Biofilm Engineering at Montana State University.
Temple University--Theses
6
Arino, Julien. "Modélisation structurée de la croissance du phytoplancton en chemostat." Phd thesis, Université Joseph Fourier (Grenoble), 2001. http://tel.archives-ouvertes.fr/tel-00002006.
Full textAbstract:
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.
7
Daoussis, Spiro. "Complicated dynamics of a three species chemostat food chain." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ30081.pdf.
Full text
8
Palmer, John. "Chemostat growth studies and bioenergetic aspects of Methanosarcina barkeri." Thesis, University of Kent, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.279877.
Full text
9
McIntyre, James John Miller. "Physiological studies of vancomycin production in continuous reactors." Thesis, University of Kent, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360971.
Full text
10
Lee, Lucy Joanna. "The response of chemostat-cultured Escherichia coli to zinc stress." Thesis, University of Sheffield, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.434956.
Full text
11
Fritsch, Coralie. "Approches probabilistes et numériques de modèles individus-centrés du chemostat." Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20062/document.
Full textAbstract:
Dans une première partie, nous proposons un nouveau modèle de chemostat dans lequel la population bactérienne est représentée de manière individu-centrée, structurée en masse, et la dynamique du substrat est modélisée par une équation différentielle ordinaire. Nous obtenons un processus markovien que nous décrivons à l'aide de mesures aléatoires. Nous déterminons, sous une certaine renormalisation du processus, un résultat de convergence en loi de ce modèle individu-centré hybride vers la solution d'un système d'équations intégro-différentielles. Dans une seconde partie, nous nous intéressons à des modèles de dynamiques adaptatives du chemostat. Nous reprenons le modèle individu-centré étudié dans la première partie, auquel nous ajoutons un mécanisme de mutation. Sous des hypothèses de mutations rares et de grande population, les résultats asymptotiques obtenus dans la première partie nous permettent de réduire l'étude d'une population mutante à un modèle de croissance-fragmentation-soutirage en milieu constant. Nous étudions la probabilité d'extinction de cette population mutante. Nous décrivons également le modèle déterministe associé au modèle individu-centré hybride avec mutation et nous comparons les deux approches, stochastique et déterministe; notamment nous démontrons qu'elles mènent au même critère de possibilité d'invasion d'une population mutante dans une population résidente.Nous présentons des simulations numériques illustrant les résultats mathématiques obtenusIn the first part, we propose a new chemostat model in which the bacterial population is mass structured and individual-based and the substrate dynamics are modelized by an ordinary differential equation. We obtain a Markovian process which we describe as random measures. We determine, under a certain normalization of the process, a result of convergence in distribution towards the solution of a system of integro-differential equations. In the second part, we are interested in adaptive dynamic models of the chemostat. We add a mutation mechanism to the individual-based model which was studied in the first part. Under rare mutations and large population size hypotheses, the asymptotical result of the first part allows us to reduce the study of the mutant population to a growth-fragmentation-washout model in a constant environment. We study the extinction probability of this mutant population. We also describe the deterministic model related to the hybrid individual-based model with mutations and we compare these two approaches (stochastic and deterministic). In particular we prove that the two approaches lead to the same invasion criteria of a mutant population in a resident population.We present numeric simulations in order to illustrate the mathematical results
12
Lemesle, Valérie. "Modélisation mathématique structurée de la croissance cellulaire en chemostat : analyse et estimation." Phd thesis, Université de Nice Sophia-Antipolis, 2004. http://tel.archives-ouvertes.fr/tel-00006502.
Full textAbstract:
L'objet de cette thèse est la formulation, l'étude de modèlesstructurés de croissance cellulaire dans un chemostat, appareil de culture de micro-organismes en laboratoire, et l'estimation de certaines variables d'état pour ces modèles. Après de bref rappels sur la biologie des espèces considérées et la présentation du dispositif expérimental, nous introduirons les modèles classiques utilisés pour décrire le chemostat ainsi que les modèles structurés prenant en compte la division cellulaire notamment. Nous construirons et étudierons alors deux modèles en équations différentielles ordinaires de dimension 3 mettant en valeur la croissance et la division d'une cellule. Nous
terminerons cette partie par la construction et l'étude d'un modèle basé sur des réactions biochimiques décrivant le stockage d'une cellule. La deuxième partie de cette thèse concerne l'estimation de certaines variables d'état. Ainsi, les notions d'observabilité et d'observateur seront introduites. Des observateurs classiques seront construits pour les modèles de croissance décrits dans la première partie. Enfin, comme en biologie les modèles sont souvent mal connus, nous construirons des estimateurs hybrides, donnant les variables d'état non mesurables en utilisant les variables mesurées et la connaissance partielle du modèle. Nous terminerons ces deux parties par d'autres applications possibles.
13
Gilfoyle, Christopher. "Interactions of light with nitrogen limitation in marine microalgae in chemostat culture." Thesis, Queen Mary, University of London, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.410145.
Full text
14
Braley, Richard. "The stability of the plasmid pJDB248 in chemostat culture of Saccharomyces cerevisiae." Thesis, University of Hertfordshire, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.283382.
Full text
15
Karbasi, Mahtab. "The stability of TOL plasmid in Pseudomonas putida grown in free and immobilized cell cultures." Thesis, University of Westminster, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337250.
Full text
16
Probert, Hollie Marie. "An investigation of the lumenal and mucosal microflora of the human colon : effects of prebiotics on bacteriology and gas generation." Thesis, University of Reading, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252247.
Full text
17
Bai, Zhonghu. "Oxidative stress in submerged cultures of a recombinant Aspergillus niger (BI-D)." Thesis, University of Strathclyde, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269893.
Full text
18
Venables, David. "Two-stage chemostat studies of hybridoma growth, nutrient utilisation and monoclonal antibody production." Thesis, University of Surrey, 1994. http://epubs.surrey.ac.uk/843436/.
Full textAbstract:
Growth and monoclonal antibody production kinetics of the hybridoma cell line NB1 were studied in batch, chemostat and two-stage chemostat culture. Growth associated production kinetics were observed in batch culture when glutamine was the first nutrient to be depleted. The growth phase was extended and production increased by supplementing the culture with extra glutamine, essential and non-essential amino acids. Monoclonal antibody was produced by the viable cell population with no evidence for its release from lysing cells. Increasing the concentration of individual amino acids in batch culture appeared to have a negative effect on cell growth and in some cases a positive effect on antibody production. The effect on production may have been indirect, due to the effect on growth rate. Under conditions of leucine and isoleucine limitation the kinetics of antibody production in batch culture were changed to growth dissociated with the majority of the antibody being produced during the decline phase of the culture. The kinetics of production were therefore dependent on the nutrient limiting growth. In single-stage chemostat culture monoclonal antibody production was negatively growth rate associated, in contrast to the positively growth associated production generally observed in batch culture. Therefore the feasibility of optimising negatively growth associated antibody production in the second stage of a two-stage chemostat was studied. Steady states in terms of cell concentration, nutrient utilisation and antibody production were observed in both stages of a two-stage chemostat. Monoclonal antibody production in both stages of a two-stage chemostat was negatively growth rate associated. Specific production rate increased with decreasing dilution rate. The specific production rate in the second stage was less than the first stage at an equivalent dilution rate even though the growth rate was less, except at dilution rates below 0.02 h-1 when the growth rate in stage two was negative. Feeding the second stage of a two-stage chemostat with amino acids increased the growth rate but decreased the specific production rate. Attempts to decrease the growth rate of a fed second stage by increasing the volume and therefore decreasing the dilution rate relative to the first stage were unsuccessful. Growth rate remained high, however volumetric production was significantly increased. The concentration of an amino acid in the medium appeared to influence its rate of utilisation in batch and chemostat culture. Increasing the concentration of an individual amino acid tended to have a negative effect on cell growth. Decreasing the concentration of an individual amino acid reduced the extent to which it was utilised. Increasing the concentration of all amino acids increased their rate of utilisation without increasing the cell concentration.
19
Beste, Dany J. V. "Analysis of a chemostat model of TB persistence using a global systems approach." Thesis, University of Surrey, 2004. http://epubs.surrey.ac.uk/843638/.
Full textAbstract:
An experimental system of Mycobacterium tuberculosis growth) in a carbon-limited chemostat, has been established using Mycobacterium bovis BCG as a model organism. In this model carbon- limited chemostats with low concentrations of glycerol were used to simulate possible growth rates during different stages of tuberculosis. A doubling time of 23 hours (D = 0.03 h-1) was adopted to represent the acute phase of infection whereas a slower dilution rate, equivalent to a doubling time of 69 hours (D = 0.01 h-1) was used to model mycobacterial persistence. Cell macromolecular (RNA, DNA, carbohydrate and lipid) and elemental (C, H, N) compositions of biomass were determined in the model, revealing an atypical bacterial cell containing large amounts of lipid and carbohydrate. The correlation of RNA content with growth rate indicated that ribosome production in carbon limited M. bovis BCG cells is subject to growth rate dependent control. These results also clearly show that the proportion of lipid in the mycobacterial cell is very sensitive to changes in the growth rate, probably reflecting changes in the amounts of storage lipids. This may have particular significance for mycobacteria during chronic TB as this stage of the disease is thought to involve a metabolic switch in the bacteria's carbon source to fats. Given the importance of isocitrate lyase in fat metabolism and the survival of persistent bacteria, an isocitrate lyase mutant of M. bovis BCG was constructed and used as a biological probe to test the validity of the chemostat model of TB persistence. The mutant strain behaved identically to the wild type at the fast growth rate but was attenuated for survival at the slower growth rate demonstrating that isocitrate lyase is important for survival in the model. Transcriptomic analysis using DNA microarrays demonstrated that 353 genes were differentially expressed between the slow and fast growing mycobacterial cells. These data show a significant shift in metabolism towards scavenging nutrients from the environment and the upregulation of several "persistence genes" in the slow growth rate. Optimization of two-dimensional electrophoresis methodology allowed the cellular protein composition of BCG in the model to be studied. Expression of 7 proteins increased and 3 proteins decreased in the slow relative to the faster growing chemostat culture. Proteins identified included the ATP-binding protein Rv2623 and Rv2626c, proteins known to be upregulated during growth in vivo. These studies demonstrated the power of combining chemostat models with global system approaches such as proteomics, transcriptomics and fluxomics technologies in deciphering the complex programme of M. tuberculosis during persistence.
20
Holroyd, Christopher Paul. "A study of bacitracin production in a chemostat with and without biomass recycle." Thesis, University of Kent, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303148.
Full text
21
Massie, Thomas Michael. "Dynamic behavior of phytoplankton populations far from steady state : chemostat experiments and mathematical modeling." Phd thesis, Universität Potsdam, 2011. http://opus.kobv.de/ubp/volltexte/2012/5810/.
Full textAbstract:
Nature changes continuously and is only seemingly at equilibrium. Environmental parameters like temperature, humidity or insolation may strongly fluctuate on scales ranging from seconds to millions of years. Being part of an ecosystem, species have to cope with these environmental changes. For ecologists, it is of special interest how individual responses to environmental changes affect the dynamics of an entire population – and, if this behavior is predictable. In this context, the demographic structure of a population plays a decisive role since it originates from processes of growth and mortality. These processes are fundamentally influenced by the environment. But, how exactly does the environment influence the behavior of populations? And what does the transient behavior look like?
As a result from environmental influences on demography, so called cohorts form. They are age or size classes that are disproportionally represented in the demographic distribution of a population. For instance, if most old and young individuals die due to a cold spell, the population finally consists of mainly middle-aged individuals. Hence, the population got synchronized. Such a population tends to show regular fluctuations in numbers (denoted as oscillations) since the alternating phases of individual growth and population growth (due to reproduction) are now performed synchronously by the majority of the population.That is, one time the population growths, and the other time it declines due to mortality. Synchronous behavior is one of the most pervasive phenomena in nature. Gravitational synchrony in the solar system; fireflies flashing in unison; coordinate firing of pacemaker cells in the heart; electrons in a superconductor marching in lockstep. Whatever scale one looks at, in animate as well as inanimate systems, one is likely to encounter synchrony. In experiments with phytoplankton populations, I could show that this principle of synchrony (as used by physicists) could well-explain the oscillations observed in the experiments, too. The size of the fluctuations depended on the strength by which environmental parameters changed as well as on the demographic state of a population prior to this change. That is, two population living in different habitats can be equally influenced by an environmental change, however, the resulting population dynamics may be significantly different when both populations differed in their demographic state before. Moreover, specific mechanisms relevant for the dynamic behavior of populations, appear only when the environmental conditions change.
In my experiments, the population density declined by 50% after ressource supply was doubled. This counter-intuitive behavior can be explained by increasing ressource consumption. The phytoplankton cells grew larger and enhanced their individual constitution. But at the same time, reproduction was delayed and the population density declined due to the losses by mortality.
Environmental influences can also synchronize two or more populations over large distances, which is denoted as Moran effect. Assume two populations living on two distant islands. Although there is no exchange of individuals between them, both populations show a high similarity when comparing their time series. This is because the globally acting climate synchronizes the regionally acting weather on both island. Since the weather fluctuations influence the population dynamics, the Moran effect states that the synchrony between the environment equals the one between the populations. My experiments support this theory and also explain deviations arising when accounting for differences in the populations and the habitats they are living in. Moreover, model simulations and experiments astonishingly show that the synchrony between the populations can be higher than between the environment, when accounting for differences in the environmental fluctuations (“noise color”).Die Natur unterliegt ständigen Veränderungen und befindet sich nur vermeintlich in einem Gleichgewicht. Umweltparameter wie Temperatur, Luftfeuchtigkeit oder Sonneneinstrahlung schwanken auf einer Zeitskala von Sekunden bis Jahrmillionen und beinhalten teils beträchtliche Unterschiede. Mit diesen Umweltveränderungen müssen sich Arten als Teil eines Ökosystems auseinandersetzen. Für Ökologen ist interessant, wie sich individuelle Reaktionen auf die Umweltveränderungen im dynamischen Verhalten einer ganzen Population bemerkbar machen und ob deren Verhalten vorhersagbar ist. Der Demografie einer Population kommt hierbei eine entscheidende Rolle zu, da sie das Resultat von Wachstums- und Sterbeprozessen darstellt. Eben jene Prozesse werden von der Umwelt maßgeblich beeinflusst. Doch wie genau beeinflussen Umweltveränderungen das Verhalten ganzer Populationen? Wie sieht das vorübergehende, transiente Verhalten aus? Als Resultat von Umwelteinflüssen bilden sich in Populationen sogenannte Kohorten, hinsichtlich der Zahl an Individuen überproportional stark vertretene Alters- oder Größenklassen. Sterben z.B. aufgrund eines außergewöhnlich harten Winters, die alten und jungen Individuen einer Population, so besteht diese anschließend hauptsächlich aus Individuen mittleren Alters. Sie wurde sozusagen synchronisiert. Eine solche Populationen neigt zu regelmäßigen Schwankungen (Oszillationen) in ihrer Dichte, da die sich abwechselnden Phasen der individuellen Entwicklung und der Reproduktion nun von einem Großteil der Individuen synchron durchschritten werden. D.h., mal wächst die Population und mal nimmt sie entsprechend der Sterblichkeit ab. In Experimenten mit Phytoplankton-Populationen konnte ich zeigen, dass dieses oszillierende Verhalten mit dem in der Physik gebräuchlichen Konzept der Synchronisation beschrieben werden kann. Synchrones Verhalten ist eines der verbreitetsten Phänomene in der Natur und kann z.B. in synchron schwingenden Brücken, als auch bei der Erzeugung von Lasern oder in Form von rhythmischem Applaus auf einem Konzert beobachtet werden. Wie stark die Schwankungen sind, hängt dabei sowohl von der Stärke der Umweltveränderung als auch vom demografischen Zustand der Population vor der Veränderung ab. Zwei Populationen, die sich in verschiedenen Habitaten aufhalten, können zwar gleich stark von einer Umweltveränderung beeinflusst werden. Die Reaktionen im anschließenden Verhalten können jedoch äußerst unterschiedlich ausfallen, wenn sich die Populationen zuvor in stark unterschiedlichen demografischen Zuständen befanden. Darüber hinaus treten bestimmte, für das Verhalten einer Population relevante Mechanismen überhaupt erst in Erscheinung, wenn sich die Umweltbedingungen ändern. So fiel in Experimenten beispielsweise die Populationsdichte um rund 50 Prozent ab nachdem sich die Ressourcenverfügbarkeit verdoppelte. Der Grund für dieses gegenintuitive Verhalten konnte mit der erhöhten Aufnahme von Ressourcen erklärt werden. Damit verbessert eine Algenzelle zwar die eigene Konstitution, jedoch verzögert sich dadurch die auch die Reproduktion und die Populationsdichte nimmt gemäß ihrer Verluste bzw. Sterblichkeit ab. Zwei oder mehr räumlich getrennte Populationen können darüber hinaus durch Umwelteinflüsse synchronisiert werden. Dies wird als Moran-Effekt bezeichnet. Angenommen auf zwei weit voneinander entfernten Inseln lebt jeweils eine Population. Zwischen beiden findet kein Austausch statt – und doch zeigt sich beim Vergleich ihrer Zeitreihen eine große Ähnlichkeit. Das überregionale Klima synchronisiert hierbei die lokalen Umwelteinflüsse. Diese wiederum bestimmen das Verhalten der jeweiligen Population. Der Moran-Effekt besagt nun, dass die Ähnlichkeit zwischen den Populationen jener zwischen den Umwelteinflüssen entspricht, oder geringer ist. Meine Ergebnisse bestätigen dies und zeigen darüber hinaus, dass sich die Populationen sogar ähnlicher sein können als die Umwelteinflüsse, wenn man von unterschiedlich stark schwankenden Einflüssen ausgeht.
22
Phongsawat, Chonticha. "Effect of nutrient limitation in chemostat cultures on amino acid excretion in Clostridium thermocellum." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-246982.
Full textAbstract:
Introduction: Clostridium thermocellum is considered a model organism for consolidated bioprocessing, due to its ability to hydrolyze lignocellulosic biomass more efficiently than many other organisms and to produce ethanol.In order to meet the industrial requirements of ethanol yield and titer, metabolic engineering efforts have been made resulting in a strain that successfully displays increased ethanol yield with reduced amount of some byproducts.However, the ethanol yield in this engineered strain still does not meet the industrial requirements and significant amounts of amino acids are still produced. To attempt to decrease the level of amino acid excretion intended to improve the ethanol yield in C. thermocellum, it is essential to understand its metabolism 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 to analyze 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 the limiting 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.Conclusions: Considering yields of total amino acids excreted in both limitations, it was hypothesized that C. thermocellum exploited the amino acid excretion to maintain carbon balance around the pyruvate node caused by excess of the carbon. Based on yield of valine excreted in particular, it was hypothesized that amino acid excretion was used to maintain redox balance in the metabolism of C. thermocellum, where malate shunt could play a major role.However, results of the Carbon-limitation did not allow any conclusion of nitrogen excess having an effect on amino acid excretion in C. thermocellum.
23
Cavaille, Laetitia. "Production de Polyhydroxybutyrates à partir d'acides gras volatils en culture ouverte : influence du degré de limitation en phosphore sur les réponses cinétiques et les sélections microbiennes." Thesis, Toulouse, INSA, 2015. http://www.theses.fr/2015ISAT0049/document.
Full textAbstract:
La production de biopolymères de type polyhydroxyalkanoates (PHA) est une alternative attractive pour remplacer, en partie, les plastiques produits à partir de ressources fossiles. Les contraintes techniques imposées par les cultures pures (substrat purifié, stérilité…) impliquent un coût de production qui rend la production de ces bioplastiques difficilement compétitive par rapport à celle des plastiques conventionnels. L’utilisation de cultures non axéniques permettrait de palier les contraintes des cultures pures mais nécessite une étape de sélection des microorganismes producteurs naturels de PHA. A partir d’un inoculum issu de boues d’épuration et de substrats de types AGV (acide butyrique et acétique), une stratégie de limitation de la croissance par le phosphore pour accumuler du PHB a été mise en place. Nous avons étudié, avec les modes de culture fed-batch et continu, le potentiel de sélection de souches productrices et de production de PHA en fonction des paramètres opératoires (taux de dilution) et environnementaux (degré de limitation en phosphore). L’objectif scientifique a consisté à améliorer les connaissances sur le rôle d’une limitation en phosphore selon les conditions opératoires du procédé, tout d’abord sur la nature des souches sélectionnées, et ensuite sur la croissance et l’accumulation de PHB. Pour cela, une démarche associant l’identification des micro-organismes en dynamique par une technique de pyroséquençage, une caractérisation cinétique des micro-organismes sélectionnés, une analyse procédé et le développement d’une modélisation cinétique a été effectué. L’objectif final du travail visait l’optimisation des procédés de production de PHB en culture non axénique : productivité, rendement, titre final en PHB mais aussi fiabilité et robustesse, en vue de définir une stratégie de production optimale de PHA. Les performances atteintes lors des cultures en fed-batch se situent parmi les meilleures de la littérature (70% de PHA) en cultures mixtes sans étape d’enrichissement préalable en microorganismes producteurs. Les résultats ont montré le rôle de la limitation phosphore sur le déclenchement de la production de PHB. En chémostat, l’analyse des paramètres macro-cinétiques, à partir des sélections microbiennes, a révélé des cinétiques de conversion du substrat carboné en PHB, biomasse catalytique et CO2 dépendantes du degré de limitation en phosphore et du taux de croissance. Le taux de phosphore intracellulaire (dépendant du taux de croissance et du degré de limitation phosphore), est le paramètre gouvernant la conversion du carbone. De plus, ce rôle a été observé pour toutes les populations sélectionnées sous limitation phosphore, démontrant un comportement universel de ces populations face à une limitation phosphore. En parallèle, des études dynamiques en batch à partir de ces populations ont permis de caractériser les paramètres cinétiques des souches, montrant une vitesse maximale de production de PHB de 0,6 et 1,2 Cmol/Cmol.h avec acide acétique et butyrique respectivement. Ces hypothèses réalisées à partir des observations expérimentales ont permis l’établissement d’un nouveau modèle cinétique basé sur le rôle du phosphore intracellulaire sur la conversion du carbone. La confrontation de ce modèle aux résultats expérimentaux a conforté et amélioré la compréhension des processus de dilution intracellulaire du phosphore et de stockage de PHB. Ce modèle a également permis d’explorer une large gamme de conditions environnementales et de prédire les comportements microbiens d’organismes producteurs et non producteurs. A partir des résultats observés et du modèle cinétique établi, les performances de différentes configurations de procédés de production de PHA ont pu être discutées : chémostat simple ou double étage, fed-batch, chémostat et batch... Les performances en termes de productivités, taux de PHB intracellulaires, degré de sélection de producteurs et robustesse du procédé sont comparéesThe production of polyhydroxyalkanoates (PHA) is an attractive alternative for plastics produced from fossil resources. The technical constraints imposed by pure cultures (purified substrate, sterilization ...) involve a high production cost of PHA production, and the production of these bioplastics is hardly competitive. The use of non-axenic cultures would avoid the constraints of pure cultures but requires a selection step of PHA producers. From a microbial inoculum (activated sludge) and AGV (butyric and acetic acid), a strategy for limiting the growth by phosphorus to accumulate PHB was established. From fed-batch and continuous culture, we studied the selection of PHA producers and the production of PHA based on operating parameters (dilution rate) and environmental (degree of phosphorus limitation). The scientific objective was to improve knowledge on the role of phosphorus limitation according to the operating conditions of the process, first about the nature of selected strains, and then about the cellular growth and PHB accumulation. For this, an approach involving identification of microorganisms by pyrosequencing method, a kinetic characterization of selected microorganisms, a process analysis and development of a kinetic modeling were performed. The ultimate goal of the work was the optimization of PHB production processes in non-axenic culture: productivity, yield, final PHB concentration but also reliability and robustness, to define an optimal production strategy of PHA. The performance achieved during the fed-batch cultures are among the best in the literature (70% PHA) in mixed cultures without enrichment step of PHA producers. The results showed the role of phosphorus limitation on the PHB production. Thus, it has been demonstrated the importance of degree of phosphorus limitation to maintain cell growth allowing enrichment in PHA producers explaining the high content of PHA obtained. From microbial selections in chemostat culture, the analysis of macro-kinetic parameters revealed conversion kinetics of the carbon substrate in PHB, catalytic biomass and CO2, dependent on the degree of phosphorus limitation and growth rate. The limits on the degree of plasticity of the intracellular phosphorus (ranging from 3.8% to 0.045%) were identified as a function of the specific growth rate. This intracellular phosphorus content (depending on the growth rate and degree of phosphorus limitation), is the parameter governing carbon conversion. Furthermore, this role of the intracellular phosphorus was observed for all populations selected under phosphorus limitation in this study, demonstrating a universal behavior of these populations face to phosphorus limitation. In parallel, dynamic studies in batch reactor from these selected populations were used to characterize the kinetic parameters of the strains, showing a maximum PHB production rate of 0.6 and 1.2 Cmol/Cmol.h with acetic acid and butyric respectively. These hypotheses made from experimental observations allowed the establishment of a new kinetic model based on the role of intracellular phosphorus on carbon conversion. The comparison of this model with experimental results has strengthened and improved the understanding of the mechanisms of intracellular phosphorus dilution and storage PHB. This model was also used to explore a wide range of environmental conditions and predict microbial behavior of PHA producers and non-producing organisms according to the operating conditions in continuous or batch reactor. From the results observed and the established kinetic model, the performance of PHA production processes of different configurations was discussed: chemostat single or two-stage, fed-batch, chemostat plus batch... The productivities, intracellular PHB content, performances of selection and the reliability of the process are compared
24
Ricão, Canelhas Monica. "Life strategies for substrate assimilation by freshwater bacterioplankton." Doctoral thesis, Uppsala universitet, Limnologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-275181.
Full textAbstract:
The availability of substrates is one of the most important environmental constraints on the diversity and functioning of microorganisms. Substrate quantity and quality as well as the metabolic features of heterotrophic microorganisms determine the efficiency, speed and type of transformation that can occur in nature. As such their interplay with the environment regulates how much carbon and energy is incorporated by bacteria and subsequently reaches higher trophic levels. In lakes the bulk substrate that is available for bacteria is composed of a complex mixture of compounds, varying in lability and distribution in the environment. This thesis addresses the coupling of organic substrates, their metabolic use and the composition and ecology of the microbial community. Controlled laboratory experiments with mixed bacterial communities in either batch cultures or chemostats were designed to shed further light on bacterial use of labile and quantitatively significant carbon compounds. I show that different amino acid substrates only exert a minor influence on bacterioplankton community composition and growth. Hence the ability to use a wide range of such abundantly produced protein monomers seems to be widespread among freshwater bacteria. In contrast, when acetate was provided as the only carbon substrate, in either pulsed or continuous amendments, this very different substrate input mode had a strong effect on bacterial community composition. Biomass yield, for example, was twice as high when acetate was given in the form of pulses rather than provided continuously. In another set of experiments, I show that the oxidation of the globally significant greenhouse gas methane is a process that can potentially take place at the water-ice interface of seasonally ice-covered lakes and was not constrained by temperature as suggested in previous studies. This work also suggests that methane oxidation in ice-covered lakes can be constrained by competition for nutrients between specialized methanotrophs and heterotrophic bacteria. Combined these studies suggest that some labile substrates cause minor selection on bacterial community structure and functioning. This probably reflects the competitive advantage of using a broad range of low molecular weight substrates. However, as in the case of methanotrophs there is specialization for a specific low molecular weight substrate such as methane. In which case, competition with other community members i.e. for nutrients can constrain methane oxidation. In both cases it might however not depend just on the availability of substrate, but also on how substrates are distributed in time and space.
25
Pawlowski, Lionel. "Modélisation de l'incorporation du carbone photosynthétique en environnement marin piloté par ordinateur." Paris 6, 2004. http://www.theses.fr/2004PA066261.
Full text
26
Cordoleani, Flora. "Représentation de la réponse fonctionnelle dans un modèle prédateur-proie : du chémostat à l'écosystème." Thesis, Aix-Marseille 2, 2011. http://www.theses.fr/2011AIX22111.
Full textAbstract:
Une des grandes problématiques en écologie est d’identifier les liens qui existent entre ce qui se passe au niveau de la physiologie et du comportement des individus et les propriétés émergentes qui apparaissent au niveau de la population et des écosystèmes dans leur globalité.Dans cette thèse, nous avons abordé cette problématique à travers la modélisation du phénomène de prédation, en nous intéressant plus particulièrement à la représentation mathématique de la réponse fonctionnelle. Cette fonction représente la quantité de proies consommées par prédateur et par unité de temps. Elle synthétiseau niveau de la population un ensemble de processus survenant à différentes échelles d’organisation. La modélisation du phénomène de prédation rencontre diverses limitations liées à la complexité de ce processus biologique, et il existe donc une forte incertitude sur la nature de la réponse fonctionnelle à utiliser.A travers l’étude d’un modèle prédateur-proie en chemostat d’une part, et l’utilisation de méthodes de changement d’échelle sur un modèle prédateur-proie en patchs d’autre part, nous avons cherché à déterminer les sources de variations dans la représentation de cette réponse.Tout d’abord, nous avons mis en évidence l’influence de la variabilité des données sur la paramétrisation de la réponse fonctionnelle ainsi que sur la robustesse des sorties du modèle. Une étude de sensibilité a également permis de montrer la forte sensibilité structurelle du modèle face à cette formulation, qui peut-être plus importante que face à des changements de paramètres.De plus, il apparait que la représentation mathématique de la réponse fonctionnelle dépend fortement de l’échelle d’observation considérée. En effet, la nature de la réponse peut être modifiée lorsque l’on passe de l’échelle d’une population à celle de la communautéOne of the major issues in ecology is to identify the links between what happens in terms of physiology and behavior of individuals and the emergent properties that appear at the population and ecosystems level. In this thesis, we addressed this problem through modeling of the phenomenon of predation, especially by focusing on the mathematical functional response representation. This function represents the amount of prey consumed by predator per unit time. It synthesizes at the population level a set processes occurring at different scales of organization. Modeling of the phenomenon of predation encounters various limitations related to the complexity of this biological process, and there is, therefore, considerable uncertainty aboutthe nature of the functional response to use.Through the study of a predator-prey model in chemostat on the one hand, and use of scaling methods in a patches predator-prey model on the other hand, we seek to determine sources of variations in therepresentation of that response.First, we demonstrated the influence of data variability on the parameterization of the functional response as well as the robustness of the model outputs. A sensitivity study has also demonstrated the high structural sensitivity of the model to the formulation of this response, which may be more important than to parameterchanges.In addition, it appears that the mathematical representation of the functional response depends strongly on the scale of observation considered. The nature of the response can, indeed, be modified when changing the scale from the population to the community level
27
Richards, Anthony O'Leary. "The dynamics of enzyme synthesis and benzoate utilisation in batch and chemostat cultures of 'Alcaligenes eutrophus'." Thesis, King's College London (University of London), 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.281773.
Full text
28
Sjöberg, Gällnö Karin. "Undersökning av fosfatsbegränsningseffekter på Escherichia coli AF1000 för bättre förståelse av 3-hydroxybutyratproduktion." Thesis, KTH, Skolan för bioteknologi (BIO), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-168989.
Full text
29
Luo, Siding. "Stochastic models of microbial communities : stochastic dynamics of quasi-neutral species in a resource-limited chemostat environment." Thesis, University of Glasgow, 2014. http://theses.gla.ac.uk/5808/.
Full textAbstract:
The most indispensable work for microbial ecologists is to develop mathematical models in order to describe microbial communities. In this aspect, a proper understanding of microorganism richness and abundance is of paramount importance. A chemostat environment is a classic open microbial community, where multiple species compete for limited nutrients, whose mathematical model has broad applications in microbiology and population biology. Generally speaking, there are four key processes that may influence the diversity: selection, speciation, drift and dispersal. The debate between niche assembly theory and neutral theory has lasted for decades about the dominant process. In term of simplicity, Hubbell's unified neutral theory of biodiversity has a distinct advantage for sampling and parameterisation. It offers a quantitative stochastic base model of island macroscopic community coupled with meta-community, where species compete in a finite environment. In this thesis, an explicit quasi-neutral chemostat model is fully devised by reconciling neutral theory and niche difference, which gives insight into how the origin, maintenance and loss of biodiversity in the local competitive community at different time scales are influenced by selection, stochastic drift and dispersal. An analysis of the deterministic dynamics is conducted to explain the niche assembly rule, and to further show that the species at the same largest fitness will be selected to coexist through life history trade-offs. These species are quasi-neutral. However, over a long period of time, stochastic drift will play a dominant role in constructing the pattern of the local communities. Without dispersal, extinction is the ultimate fate of stochastic drift. Both analytical and numerical methods established in this thesis verify that the quasi-neutral species are in fact not competitively equivalent. Their difference will drive a superior species to fix in the isolated community. When dispersal is incorporated, even with low immigration rate, it will drive the long term drift of large communities, and balance extinction to maintain the diversity of the local communities. An explicit results for the stationary abundance distribution is calculated, which helps to demonstrate a deviation from the neutral model. These results from the explicit stochastic model highlight the importance of incorporating species interaction into the basic neutral model.
30
Hajji, Miled El. "Modélisation et analyse mathématiques pour les écosystèmes microbiens : approche par les systèmes dynamiques." Thesis, Montpellier 2, 2010. http://www.theses.fr/2010MON20117/document.
Full textAbstract:
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 batchCette 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
31
Tulsiani, Urvi Kotak. "Factors influencing natural attenuation of dinitrotoluenes in surface soils: Badger Army Ammunition Plant a case study." Thesis, Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/7196.
Full textAbstract:
Factors influencing natural attenuation of dinitrotoluenes (DNT) in surface soils and the application of monitored natural attenuation (MNA) as a remediation strategy were examined using contaminated soils from Badger Army Ammunition Plant (BAAP). Based on the previous research involving contaminated media obtained from locations at BAAP, and the fact that groundwater at the site is not contaminated, it seemed likely that aerobic biodegradation of DNT is active without intervention, and that natural attenuation may be an effective strategy for managing the contamination that exists at BAAP. Microcosms showed that microbes indigenous to soils are capable of 2,4-DNT mineralization and that DNT will adsorb reversibly and become bioavailable. In column studies 2,4-DNT biodegradation was observed and the nitrite evolved during DNT degradation was presumably removed due to oxidation by nitrite oxidizers. The use of simulated rainwater as influent with no nutrient amendments suggests that nutrients do not limit the biodegradation of low concentrations of DNT in the soil tested. In the chemostat study carried out to study effect lowering of temperature (22㬠15㬠10㬠7.5㠡nd 4㩠on biodegradation of DNT at hydraulic retention time of 2.5 days, no sustained change in the DNT substrate removal was observed with change in temperature, but it had a large effect on the nitrite oxidizers. This suggests that the seasonal fluctuations in temperature will have minimal effect on the DNT removal via biodegradation at temperatures above 0㮠Nitrite oxidizers were active at 22㬠their activity decreased at 15㠡nd ceased at temperatures 10㠡nd lower. Nitrite is generally taken as a line of evidence for biodegradation of DNT. The results from the soil column study and chemostat showed that nitrite measurement should not be always taken as a conclusive indicator of DNT degradation. It should be taken into consideration that absence of nitrite does not necessarily mean absence of DNT biodegradation (probably at high temperatures).
32
Jin, Jian. "Kinetic study of biomass and hydrocarbon production in chemostat cultures of the microalga Botryococcus braunii : a physiological approach." Nantes, 2016. http://archive.bu.univ-nantes.fr/pollux/show.action?id=0625ba31-c1a0-4960-9b0d-cf94f96fcd99.
Full textAbstract:
L'espèce Botryococcus braunii a la propriété d'accumuler des quantités importantes d'hydrocarbures à longue chaîne. L’objectif est d'étudier les effets de variables opératoires en photobioréacteur sur les productivités en biomasse et hydrocarbures de cultures continues de deux souches de B. Braunii, l’une de race A et l’autre de race B accumulant respectivement soit des alkadiènes et alkatriènes soit des botryococcènes. Les deux principaux hydrocarbures contenus dans la biomasse de la souche de race A SAG 30. 81, sont identifiés comme étant le nonacosadiene et l’hentriacontadiene. L’analyse d’états stationnaires successifs montre que ses productivités en biomasse et hydrocarbures sont pH-dépendantes avec un optimum à pH 6. 5, effet corrélé à la concentration résiduelle en CO2 (aq) des cultures. Par contre, le taux de croissance spécifique, le flux lumineux et l’approvisionnement en azote ne modifient pas les teneurs en hydrocarbures. Les données répondent au modèle de Luedeking-Piret, confirmant que les cinétiques de production des hydrocarbures sont principalement associées à la croissance des cultures et à une surproduction en lipides intracellulaires, indépendamment du taux d’azote du milieu de culture ou du flux lumineux. Les productivités en biomasse, hydrocarbures et lipides intracellulaires sont plus élevées avec la souche de race B BOT 22. Les teneurs significativement plus élevées en acides gras totaux et en acide oléique de la souche SAG 30. 81 semblent indicatrices des voies différentes de biosynthèse des hydrocarbures des deux souches. Ces caractéristiques physiologiques sont discutées dans la perspective de la sélection de conditions optimales d’exploitationThe microalgal species Botryococcus braunii is attracting particular interest due to its ability to accumulate large amounts of long-chain hydrocarbons in an extracellular matrix. This study aimed to investigate the effects of operative factors on biomass and hydrocarbon production of two strains within the continuous cultures at successive steady-states in a controlled PBR. A comparative study was carried out on a race A strain and a race B strain, accumulating respectively either the alkadienes and alkatrienes or botryococcenes hydrocarbons. The predominant hydrocarbons in the race A strain SAG 30. 81 were determined as nonacosadiene and hentriacontadiene. Its biomass and hydrocarbon productivities were shown to be pH-dependent with an optimum at pH 6. 5. This effect was related to the dissolved CO2 concentration. Data from successive steady-states confirmed, according to the Luedeking-Piret model, that the hydrocarbon production is mainly growth associated, whatever nitrogen conditions. By contrast, the hydrocarbon content was relative constant irrespective of growth rates, light intensity and nitrogen conditions. Intracellular lipids were overproduced even in nitrogen sufficient conditions at high specific light supply. Higher biomass, hydrocarbon and lipids productivities were obtained with the race B strain BOT 22 than with the race A strain SAG 30. 81. The total fatty acids and oleic acid contents in race A were significantly higher than in race B, supporting their respective hydrocarbons biosynthesis pathways. These physiological features are discussed in view of the selection of optimal operative conditions for efficient hydrocarbon production by microalgae
33
Schmidt, Julia K. "Quantitative experimental characterization and mathematical modeling of mixed culture dynamics analysis of a medically relevant three-species mixed culture in a chemostat." Aachen Shaker, 2008. http://d-nb.info/992243750/04.
Full text
34
Haidar, Ihab. "Dynamiques microbiennes et modélisation des cycles biogéochimiques terrestres." Thesis, Montpellier 2, 2011. http://www.theses.fr/2011MON20202.
Full textAbstract:
Cette thèse adresse des problèmes liés à la modélisation des écosystèmes microbiens dans les sols.Les modèles de transport réactif sont très performants pour modéliser la biogéochimie d'un milieu poreux variablement saturé en tenant compte de plusieurs paramètres physiques et géochimiques mais ils n'intègrent pas (ou sinon de facon très sommaire) les activités microbiologiques dans les sols. Le modèle mathématique du chemostat est couramment utilisé en écologie microbienne. Dans le but d'une représentation spatiale plus simplifiée que les modèles de transport réactif mais suffisamment pertinente pour rendre compte de phénomènes biologiques, cette thèse est une première tentative pour comprendre la fonction entrées-sorties dans un chemostat structuré, et étudier comment une structure spatiale peut modifier cette fonction, et quels sont les paramètres clésThe aim of this thesis is to study some problems related to the modeling of microbial ecosystems in soil. Considering different physical and biogeochemical parameters, the reactif transport models are very performing to represent the biochemistry of a variably saturated porous media. In contrast, these models don't integrate (or sparsely) the microbiological activities in the soils. The mathematical model of chemostat is frequently used in microbial ecology. For the purpose of a more simplified spatial representation than the reactif transport models, but sufficiently relevant to represent biological phenomena, this thesis is a first attempt to understand the "input-output" function in a structured chemostat, and to study how a special structure can alter this function, and what are the key parameters
35
Seipel, Kurtz. "Continuous growth and heat shock of thermoacidophilic Sulfolobus in a triple-stage chemostat for overexpression and isolation of chaperonin." Thesis, University of Iowa, 2012. https://ir.uiowa.edu/etd/2981.
Full text
36
Tulsiani, Urvi Kotak. "Factors influencing natural attenuation of dinitrotoluenes in surface soils : badger army ammunition plants : a case study." Available online, Georgia Institute of Technology, 2005, 2005. http://etd.gatech.edu/theses/available/etd-07142005-000016/.
Full text
37
Henry, Leigh-Anne. "Partitioning Between Soil-Adsorbed and Planktonic Escherichia coli." Thesis, Virginia Tech, 2004. http://hdl.handle.net/10919/32255.
Full textAbstract:
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 E. coli 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 E. coli partitioning. The E. coli 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 E. coli under different environmental conditions are recommended in order to better understand attachment prior to modeling attached and planktonic E. coli separately.
Master of Science
38
Riquelme, Victor. "Optimal control problems for bioremediation of water resources." Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT290/document.
Full textAbstract:
Cette thèse se compose de deux parties. Dans la première partie, nous étudions les stratégies de temps minimum pour le traitement de la pollution dans de grandes ressources en eau, par exemple des lacs ou réservoirs naturels, à l'aide d'un bioréacteur continu qui fonctionne à un état quasi stationnaire. On contrôle le débit d'entrée d'eau au bioréacteur, dont la sortie revient à la ressource avec le même débit. Nous disposons de l'hypothèse d'homogénéité de la concentration de polluant dans la ressource en proposant trois modèles spatialement structurés. Le premier modèle considère deux zones connectées l'une à l'autre par diffusion et seulement une d'entre elles connectée au bioréacteur. Avec l'aide du Principe du Maximum de Pontryagin, nous montrons que le contrôle optimal en boucle fermée dépend seulement des mesures de pollution dans la zone traitée, sans influence des paramètres de volume, diffusion, ou la concentration dans la zone non traitée. Nous montrons que l'effet d'une pompe de recirculation qui aide à homogénéiser les deux zones est avantageux si opérée à vitesse maximale. Nous prouvons que la famille de fonctions de temps minimal en fonction du paramètre de diffusion est décroissante. Le deuxième modèle consiste en deux zones connectées l'une à l'autre par diffusion et les deux connectées au bioréacteur. Ceci est un problème dont l'ensemble des vitesses est non convexe, pour lequel il n'est pas possible de prouver directement l'existence des solutions. Nous surmontons cette difficulté et résolvons entièrement le problème étudié en appliquant le principe de Pontryagin au problème de contrôle relaxé associé, obtenant un contrôle en boucle fermée qui traite la zone la plus polluée jusqu'au l'homogénéisation des deux concentrations. Nous obtenons des limites explicites sur la fonction valeur via des techniques de Hamilton-Jacobi-Bellman. Nous prouvons que la fonction de temps minimal est non monotone par rapport au paramètre de diffusion. Le troisième modèle consiste en deux zones connectées au bioréacteur en série et une pompe de recirculation entre elles. L'ensemble des contrôles dépend de l'état, et nous montrons que la contrainte est active à partir d'un temps jusqu'à la fin du processus. Nous montrons que le contrôle optimal consiste à l'atteinte d'un temps à partir duquel il est optimal de recirculer à vitesse maximale et ensuite ré-polluer la deuxième zone avec la concentration de la première. Ce résultat est non intuitif. Des simulations numériques illustrent les résultats théoriques, et les stratégies optimales obtenues sont testées sur des modèles hydrodynamiques, en montrant qu'elles sont de bonnes approximations de la solution du problème inhomogène. La deuxième partie consiste au développement et l'étude d'un modèle stochastique de réacteur biologique séquentiel. Le modèle est obtenu comme une limite des processus de naissance et de mort. Nous établissons l'existence et l'unicité des solutions de l'équation contrôlée qui ne satisfait pas les hypothèses habituelles. Nous prouvons que pour n'importe quelle loi de contrôle la probabilité d'extinction de la biomasse est positive. Nous étudions le problème de la maximisation de la probabilité d'atteindre un niveau de pollution cible, avec le réacteur à sa capacité maximale, avant l'extinction. Ce problème ne satisfait aucune des suppositions habituelles (la dynamique n'est pas lipschitzienne, diffusion dégénérée localement hölderienne, contraintes d'état, ensembles cible et absorbant s'intersectent), donc le problème doit être étudié dans deux étapes: en premier lieu, nous prouvons la continuité de la fonction de coût non contrôlée pour les conditions initiales avec le volume maximal et ensuite nous développons un principe de programmation dynamique pour une modification du problème original comme un problème de contrôle optimal avec coût final sans contrainte sur l'étatThis thesis consists of two parts. In the first part we study minimal time strategies for the treatment of pollution in large water volumes, such as lakes or natural reservoirs, using a single continuous bioreactor that operates in a quasi-steady state. The control consists of feeding the bioreactor from the resource, with clean output returning to the resource with the same flow rate. We drop the hypothesis of homogeneity of the pollutant concentration in the water resource by proposing three spatially structured models. The first model considers two zones connected to each other by diffusion and only one of them treated by the bioreactor. With the help of the Pontryagin Maximum Principle, we show that the optimal state feedback depends only on the measurements of pollution in the treated zone, with no influence of volume, diffusion parameter, or pollutant concentration in the untreated zone. We show that the effect of a recirculation pump that helps to mix the two zones is beneficial if operated at full speed. We prove that the family of minimal time functions depending on the diffusion parameter is decreasing. The second model consists of two zones connected to each other by diffusion and each of them connected to the bioreactor. This is a problem with a non convex velocity set for which it is not possible to directly prove the existence of its solutions. We overcome this difficulty and fully solve the studied problem applying Pontryagin's principle to the associated problem with relaxed controls, obtaining a feedback control that treats the most polluted zone up to the homogenization of the two concentrations. We also obtain explicit bounds on its value function via Hamilton-Jacobi-Bellman techniques. We prove that the minimal time function is nonmonotone as a function of the diffusion parameter. The third model consists of a system of two zones connected to the bioreactor in series, and a recirculation pump between them. The control set depends on the state variable; we show that this constraint is active from some time up to the final time. We show that the optimal control consists of waiting up to a time from which it is optimal the mixing at maximum speed, and then to repollute the second zone with the concentration of the first zone. This is a non intuitive result. Numerical simulations illustrate the theoretical results, and the obtained optimal strategies are tested in hydrodynamic models, showing to be good approximations of the solution of the inhomogeneous problem. The second part consists of the development and study of a stochastic model of sequencing batch reactor. We obtain the model as a limit of birth and death processes. We establish the existence and uniqueness of solutions of the controlled equation that does not satisfy the usual assumptions. We prove that with any control law the probability of extinction is positive, which is a non classical result. We study the problem of the maximization of the probability of attaining a target pollution level, with the reactor at maximum capacity, prior to extinction. This problem does not satisfy any of the usual assumptions (non Lipschitz dynamics, degenerate locally H"older diffusion parameter, restricted state space, intersecting reach and avoid sets), so the problem must be studied in two stages: first, we prove the continuity of the uncontrolled cost function for initial conditions with maximum volume, and then we develop a dynamic programming principle for a modification of the problem as an optimal control problem with final cost and without state constraint
39
Yayo, Johannes. "Growth of Clostridium thermocellum on glucose and fructose." Thesis, KTH, Skolan för bioteknologi (BIO), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-215233.
Full text
40
Coello, Nereida. "Production de L-lysine par un mutant de Corynebacterium glutamicum : quelques aspects physiologiques." Compiègne, 1990. http://www.theses.fr/1990COMPD292.
Full textAbstract:
Cette étude concerne l'effet des limitations nutritionnelles (phosphore, potassium, magnésium et carbone) sur la croissance des microorganismes et la production de L-lysine en cultures discontinue et continue. Il y a un rapport étroit entre l'effet d'une limitation, le taux de croissance du micro-organisme et le déclenchement de la production de L-lysine. Quel que soit leur état physiologique, les cellules possèdent une capacité potentielle de production de L-lysine. Cette production est favorisée lorsque les conditions environnementales le permettent. On a observé que lorsqu'une culture limitée par P, K, et Mg est à faible taux de croissance (0,015-0,03 h-1), la production est déclenchée. L'étude enzymatique montre qu'une activité 6-P-gluconate déshydrogénase élevée est associée aux états physiologiques de production. On n'a détecté aucune activité pyruvate carboxylase chez la souche MG. De grandes variations dans les activités des enzymes telles que l'isocitrate déshydrogénase, la phosphoénolpyruvate carboxylase et la citrate synthétase ont été observées dans les états physiologiques étudiés. Les micro-organismes peuvent réguler leur statut énergétique non seulement par la surproduction métabolique, mais aussi par l'accumulation de matériels de réserve. La présence de granules de polyphosphates a été observée dans le cytoplasme des cellules en état de production. La présence de granules de glycogène a été mise en évidence dans les cellules cultivées en chemostat et limitées en phosphore. La spectrométrie de masse a été utilisée pour confirmer l'absence de PHB chez la souche MG. Les recherches effectuées sur la souche MG ont permis d'établir un rapport entre les données de cinétique de fermentation et certaines activités enzymatiques concernant la production de L-lysine, et ceci dans le but de donner aux paramètres cinétiques obtenus une signification physiologique.
41
Settele, Anja. "Untersuchungen episodischer Kleingewässer unter besonderer Berücksichtigung der temporären Epibiosis des Rädertieres Brachionus rubens Ehrenberg 1838 auf der Cladocere Moina brachiata Jurine 1820." Ulm : Universität Ulm, Fakultät für Naturwissenschaften, 2003. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB11612115.
Full text
42
Mercier, Claire J. M. "A genome-scale investigation of clavulanic acid biosynthesis by Streptomyces clavuligerus in batch and chemostat cultures using transcriptomic and fluxomic analysis." Thesis, University of Surrey, 2007. http://epubs.surrey.ac.uk/842706/.
Full textAbstract:
Streptomyces clavuligerus produces the potent beta-lactamase inhibitor clavulanic acid, which is used in conjunction with other beta-lactam antibiotics. Although the genome of S. davuligerus has not yet been sequenced, tools were developed to study the metabolic flux distribution (fluxomics) and gene expression (transcriptomics) at genome scale. A Streptomyces clavuligerus-specific genome-scale metabolic network was derived from the network reconstructed for the close relative S. coelicolor (Borodina et al., 2005), removing reactions unique to S. coelicolor and adding the ones known to take place in S. clavuligerus. This metabolic network was then used to perform Flux Balance Analysis. Genome-scale transcription analysis was also made possible by customising S. coelicolor DNA microarrays thanks to the addition of 80 S. clavuligerus-specific probes, corresponding to most of the sequenced S. clavuligerus genes, to the 8,000 S. coelicolor probes, including probes for the genes of the clavulanic acid cluster. These genome- scale methodologies were applied to S. clavuligerus grown in chemostat and batch cultures. Macromolecular compositions at two dilution rates (0.02h-1 and 0.05h-1) and in different growth phases were analysed in order to obtain reliable flux data. Flux distribution was simulated accurately and predicted supplements such as threonine, malate, pyruvate or citrate that might lead to increased antibiotic production. The customised DNA microarrays demonstrated that the genes of the clavulanic acid cluster are regulated differently in batch and in chemostat culture. The analysis of the transcription data also predicted that the use of supplements such as glycine or thymidine could lead to increased clavulanic acid production. Finally, the gene expression patterns showed that S. clavuligerus might be using an alternative pathway to metabolise glycerol during clavulanic acid production. In batch culture, the fluxomic and transcriptomic data showed no correlation, while some correlation was observed in chemostat culture. This demonstrated that chemostat culture is more useful than batch culture when performing genome-scale analysis. However, batch culture remains a valuable tool to assess gene co-expression or to study a switch between two phases of growth.
43
Argyropoulos, Dimitris. "Stability of plasmid pPFF1 in recombinant Bacillus subtilis cultures and the effect of batch, chemostat and cyclic fed batch fermentation systems." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265716.
Full text
44
Massie, Thomas Michael [Verfasser], and Ursula [Akademischer Betreuer] Gaedke. "Dynamic behavior of phytoplankton populations far from steady state : chemostat experiments and mathematical modeling [[Elektronische Ressource]] / Thomas Michael Massie. Betreuer: Ursula Gaedke." Potsdam : Universitätsbibliothek der Universität Potsdam, 2012. http://d-nb.info/1020527897/34.
Full text
45
Tong, Jeremy Michael. "An investigation into the physiology of a Chinese hamster ovary cell one producing recombinant human interferon-#gamm# using inhibition and chemostat studies." Thesis, University of Kent, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358204.
Full text
46
Timoumi, Asma. "Study of the dynamics of physiological and metabolic responses of Yarrowia lipolytica to environmental physico-chemical perturbations." Thesis, Toulouse, INSA, 2017. http://www.theses.fr/2017ISAT0009/document.
Full textAbstract:
En raison des capacités de mélange limitantes, des hétérogénéités au sein des bioréacteurs se produisent régulièrement lors de l’extrapolation à l’échelle industrielle. En conséquence, les microorganismes circulant au sein de ces bioréacteurs sont continuellement exposés à des gradients locaux au niveau des paramètres fondamentaux du procédé tel que le pH, la température, la concentration en substrat et en oxygène dissous. Ces fluctuations micro-environnementales peuvent affecter la croissance, le métabolisme et la morphologie des cellules, en fonction de la nature, de l’intensité, de la durée et/ou de la fréquence de la perturbation rencontrée. L’objectif de ce travail est l’étude quantitative de l’impact des fluctuations de pH et d’oxygène dissous sur le comportement dynamique de Yarrowia lipolytica, une levure avec un potentiel biotechnologique prometteur, aussi bien aux niveaux morphologique que métabolique. Pour répondre à cet objectif, des cultures en bioréacteur en conditions d’environnement contrôlé ont été mises en œuvre afin d’établir un lien de causalité directe entre la perturbation et la réponse observée. L’implémentation de deux modes de cultures différents (batch et chemostat) a permis de caractériser le comportement dynamique des populations cellulaires dans des états physiologiques différents: En mode continu, toutes les cellules sont dans le même état physiologique et se multiplient à la même vitesse de croissance, tandis que des sous-populations de levures dans des états physiologiques distincts peuvent cohabiter dans les cultures en mode batch. Un effort important a été consacré au développement et validation des méthodes pour une quantification rigoureuse des évolutions morphologiques de Y. lipolytica à l’échelle de la population. Le comportement macroscopique de la levure a été caractérisé par l’évaluation des dynamiques de croissance, la viabilité, les vitesses de consommation du glucose et d’oxygène, ainsi que les vitesses de production d’acide organique et de dioxyde de carbone. Trois techniques, à savoir la cytométrie en flux (CYT), la morpho-granulométrie (MG) et la diffraction dynamique de la lumière (DLS) ont été employé pour la quantification du phénomène d’élongation. Les résultats obtenus démontrent qu’il n’y a pas d’effet significatif des fluctuations de pH et d’oxygène dissous sur le comportement macroscopique (vitesses spécifiques, rendements, viabilité) de la levure. Néanmoins, une transition micellaire a été induite en réponse aux deux facteurs de stress (pH and pO2) seulement en conditions d’excès de glucose, suggérant ainsi un impact de la concentration résiduelle de glucose sur la régulation de dimorphisme chez Y. lipolytica. Le contrôle et la régulation de la concentration de glucose dans le milieu peut contribuer à une meilleure maitrise des changements morphologiques de Y. lipolytica en réponse à des stimuli de l’environnementDue to limited mixing capacities, heterogeneities regularly occur when scaling-up bioreactors for large-scale production. Microbial cultures are continuously exposed to local gradients in fundamental process parameters such as substrate, pH, temperature and dissolved oxygen DO concentration. These micro-environmental fluctuations may have detrimental effects on cellular growth, metabolism and morphology, depending on the nature, intensity, duration and/or frequency of the fluctuations encountered. The aim of this study was to investigate the impact of pH and DO fluctuations on the dynamic behavior of Yarrowia lipolytica, a microorganism with a promising biotechnological potential, at both morphological and metabolic levels. For this purpose, batch and continuous cultivations modes were preferentially adopted, as it enabled respectively, the study of the stress response of yeast populations growing at their maximum specific rate, and at various controlled specific growth rates in physiological steady-states. In addition, an important effort was devoted to the development and validation of morphological methods in order to acquire quantitative characterization of the response dynamics at the population scale. The macroscopic behavior of Y. lipolytica was assessed through examining the patterns of growth, viability, glucose uptake, oxygen consumption, organic acid and carbon dioxide production rates. Changes in the yeast morphology were characterized at the cell population level by means of flow cytometry, morphogranulometry and diffraction light scattering techniques. The results reflected no significant effect of pH and DO fluctuations on the macroscopic behavior (specific rates, yields, viability) of the yeast. Nevertheless, mycelial growth was induced upon exposure to both stressors, only in glucose-excess environments, suggesting therefore an impact of glucose levels on the regulation of dimorphic transition in Y. lipolytica. Controlling residual glucose concentrations in Y. lipolytica fermentations may contribute to a better monitoring of its morphological changes in response to environmental stimuli. Such data would help to optimize bioprocess performances at the industrial scale since it alleviates physico-chemical impacts due to filamentous cells
47
Lagasquie, Gabriel. "Etude du comportement en temps long de processus de markov déterministes par morceaux." Thesis, Tours, 2018. http://www.theses.fr/2018TOUR4004/document.
Full textAbstract:
L’objectif de cette thèse est d’étudier le comportement en temps long de certains processus de Markov déterministes par morceaux (PDMP) dont le flot suivi par la composante spatiale commute aléatoirement entre plusieurs flots possédant un unique équilibre attractif (éventuellement le même pour chaque flot). Nous donnerons dans un premier temps un exemple d’étude d’un tel processus construit dans le plan à partir de flots associés à des équations différentielles linéaires stables où il est déjà possible d’observer des comportements contre-intuitifs. La deuxième partie de ce manuscrit est dédiée à l’étude et la comparaison de deux modèles de compétition pour une ressource dans un environnement hétérogène. Le premier modèle est un modèle alétoire simulant l’hétérogénéité temporelle d’un environnement sur les espèces en compétition à l’aide d’un PDMP. Son étude utilise des outils maintenant classiques sur l’étude des PDMP. Le deuxième modèle est un modèle déterministe (présentant sous forme d’un système d’équations différentielles) modélisant l’impact de l’hétérogénéité spatiale d’un environnement sur ces mêmes espèces. Nous verrons que malgré leur nature très différente, le comportement en temps long de ces deux systèmes est relativement similaire et est essentiellement déterminé par le signe des taux d’invasion de chacune des espèces qui sont des quantités dépendant exclusivement des paramètres du système et modélisant la vitesse de croissance (ou de décroissance) de ces espèces lorsqu’elles sont au bord de l’extinctionThe objective of this thesis is to study the long time behaviour of some piecewise deterministic Markov processes (PDMP). The flow followed by the spatial component of these processes switches randomly between several flow converging towards an equilibrium point (not necessarily the same for each flow). We will first give an example of such a process built in the plan from two linear stable differential equations and we will see that its stability depends strongly on the switching times. The second part of this thesis is dedicated to the study and comparison of two competition models in a heterogeneous environment. The first model is a probabilistic model where we build a PDMP simulating the effect of the temporal heterogeneity of an environment over the species in competition. Its study uses classical tools in this field. The second model is a deterministic model simulating the effect of the spatial heterogeneity of an environment over the same species. Despite the fact that the nature of the two models is very different, we will see that their long time behavior is very similar. We define for both model several quantities called invasion rates modelizing the growth (or decreasing) rate speed of a species when it is near to extinction and we will see that the signs of these invasion rates fully describes the long time behavior for both systems
48
Li, Hsin-Fen. "APPLICATION OF THIN FILM ANALYSIS TECHNIQUES AND CONTROLLED REACTION ENVIRONMENTS TO MODEL AND ENHANCE BIOMASS UTILIZATION BY CELLULOLYTIC BACTERIA." UKnowledge, 2012. http://uknowledge.uky.edu/cme_etds/13.
Full textAbstract:
Cellulose from energy crops or agriculture residues can be utilized as a sustainable energy resource to produce biofuels such as ethanol. The process of converting cellulose into solvents and biofuels requires the saccharification of cellulose into soluble, fermentable sugars. However, challenges to cellulosic biofuel production include increasing the activity of cellulose-degrading enzymes (cellulases) and increasing solvent (ethanol) yield while minimizing the co-production of organic acids. This work applies novel surface analysis techniques and fermentation reactor perturbations to quantify, manipulate, and model enzymatic and metabolic processes critical to the efficient production of cellulosic biofuels.
Surface analysis techniques utilizing cellulose thin film as the model substrate are developed to quantify the kinetics of cellulose degradation by cellulase as well as the interactions with cellulase at the interfacial level. Quartz Crystal Microbalance with Dissipation (QCM-D) is utilized to monitor the change in mass of model cellulose thin films cast. The time-dependent frequency response of the QCM simultaneously measures both enzyme adsorption and hydrolysis of the cellulose thin film by fungal cellulases, in which a significant reduction in the extent of hydrolysis can be observed with increasing cellobiose concentrations. A mechanistic enzyme reaction scheme is successfully applied to the QCM frequency response for the first time, describing adsorption/desorption and hydrolysis events of the enzyme, inhibitor, and enzyme/inhibitor complexes. The effect of fungal cellulase concentration on hydrolysis is tested using the QCM frequency response of cellulose thin films. Atomic Force Microscopy (AFM) is also applied for the first time to the whole cell cellulases of the bacterium C. thermocellum, where the effect of temperature on hydrolysis activity is quantified.
Fermentation of soluble sugars to desirable products requires the optimization of product yield and selectivity of the cellulolytic bacterium, Clostridium thermocellum. Metabolic tools to map the phenotype toward desirable solvent production are developed through environmental perturbation. A significant change in product selectivity toward ethanol production is achieved with exogenous hydrogen and the addition of hydrogenase inhibitors (e.g. methyl viologen). These results demonstrate compensatory product formation in which the shift in metabolic activity can be achieved through environmental perturbation without permanent change in the organism’s genome.
49
Taciro, Marilda Keico. "Processo contínuo de produção de polihidroxialcanoatos de cadeia média (PHAMCL) sob limitação múltipla de nutrientes." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-14012009-091928/.
Full textAbstract:
A produção de PHAMCL por Pseudomonas putida IPT 046 em cultivo contínuo sob limitação múltipla de nutrientes foi estudada, utilizando glicose e frutose como fontes de carbono. O estudo da limitação em nitrogênio, fósforo e simultânea de nitrogênio e fósforo para indução de acúmulo de polihidroxialcanoato, apontou que maiores valores de polímero foram acumulados quando fósforo foi o nutriente limitante (70%). Limitação em nitrogênio resultou no máximo em 40% de polímero. A limitação simultânea de nitrogênio e fósforo resultou em 68% de polímero, menor consumo de oxigênio para gerar células e maior fator de conversão de fonte de carbono em polímero (0,19 g/g) quando comparado com a limitação em fósforo, 0,16 g/g, ou à limitação em nitrogênio, 0,10 g/g. Oxigênio utilizado para manutenção das células não dependeu do tipo de limitação e dos valores das vazões específicas de alimentação. Um modelo metabólico foi proposto, ajustando aos dados experimentais na condição de limitação em nitrogênio.Multiple nutrient limited growth of Pseudomonas putida IPT 046 was studied in chemostat culture from glucose and fructose as carbon source. Nitrogen, phosphorus and both nitrogen and phosphorus limitation was performed in order to accumulate medium-chain-length polhydroxyalkanoate. Phosphorus limitation resulted in higher polymer content accumulated (70%). Nitrogen limited assays achieved only 40% of polymer. Nitrogen and phosphorus simultaneous limitation resulted in 68 % polymer content, less oxygen demand to synthesize cells and best yields of carbon into polymer (0,19 g/g) when compared with 0,16 g/g on phosphorus limitation and 0,10 g/g on nitrogen limitation. Oxygen demand for maintenance is the same, independent of limitation strategy or dilution rate performed. A metabolic pathway model was proposed and fitted with nitrogen limited experimental data.
50
Fraga, Muller Jocelyn Lisa. "The Role of Multidrug Efflux Pumps in the Stress Response of Pseudomonas aeruginosa to Organic Contamination." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/28854.
Full textAbstract:
Natural microbial communities are the ultimate drivers of change in any ecosystem. Through chemical contamination of natural environments, these communities are exposed to many different types of chemical stressors; however, research on whole genome responses to this contaminant stress is limited. This research examined the stress response of a common soil bacterium, Pseudomonas aeruginosa, to a common environmental pollutant, pentachlorophenol (PCP). In the first part of the research, it was revealed that nutrient-limited P. aeruginosa is able to respond to PCP with minimal physiological damage due to the upregulation of multidrug efflux pumps. Further study of this PCP-mediated induction of efflux pumps revealed a simultaneous increase in antibiotic resistance. It was discovered that the resistance nodulation-cell division (RND) efflux pump, MexAB-OprM, in particular is responsible for the PCP-induced increase in antibiotic resistance.
Both whole cell physiological indicators and whole genome analysis were used to examine the stress response of P. aeruginosa to PCP. Cells were grown in a chemostat at a low growth rate to simulate nutrient-limiting growth in the natural environment. Whole cell acetate uptake rates (WAUR) and viable cell counts as colony forming units (CFU) were determined as cells were exposed to increasing concentration of PCP. At the same time, changes in gene expression were examined by Affymetrix microarray technology. Results showed little change in whole-cell physiology, with no difference in WAUR and only a slight reduction in CFU. However, the microarrays revealed that over 100 genes either increased or decreased expression greater than two-fold due to the PCP exposure. In particular, multiple multidrug efflux genes were upregulated in response to the PCP. The results were validated by real time reverse transcription polymerase chain reaction (RT-PCR) for one of these genes. Further analysis of the effects of MexAB-OprM showed that this particular efflux pump is essential for the response of P. aeruginosa to the toxin PCP.
Induction of multidrug efflux pumps is responsible for the development of antibiotic resistance in strains of P. aeruginosa. Therefore, it was investigated whether PCP might induce resistance to a variety of antibiotics. The research was further extended to examine the effect of a variety of organic contaminants on MexAB-OprM efflux and antibiotic resistance development. PCP, 2,4-dinitrophenol, benzoate and Roundup® all induced antibiotic resistance. However, although MexAB-OprM is required for optimal growth in the presence of all chemicals, this particular efflux pump is only involved in increased resistance with PCP. This was confirmed using RT-PCR as mexB expression was induced by PCP, but not by the other three chemicals. A long term generational study on the effects of PCP did not result in a stable antibiotic-resistant phenotype; however, RT-PCR showed that mexB induction is a direct result of PCP exposure and can be reversed by removal of PCP.
Together, these results demonstrate the necessity to understand functional responses to contaminant stress. Discovery of direct induction of multidrug efflux pumps and the resulting increase in antibiotic resistance has significant implications for environmental microbiology and public health. This research suggests that organic contamination may result in antibiotic resistance and that antibiotic resistant strains may have a survival advantage in contaminated environments.Ph. D.