Thesis (Ph. D)--Ohio State University, 2003. / Title from first page of PDF file. Document formatted into pages; contains xvi, 196 p.: ill. Includes abstract and vita. Advisor: Herbert W. Ockerman, Dept. of Animal Science. Includes bibliographical references (p. 185-196).

Thesis (Ph. D.)--University of Alberta, 2009. / Title from pdf file main screen (viewed on Sept. 24, 2009). "A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Engineering, Department of Chemical and Materials Engineering, University of Alberta." Includes bibliographical references.

Thesis (M.Sc.)--Memorial University of Newfoundland, 1997. / Restricted until May 1998. Bibliography: leaves 90-102.

Submitted by Nathália Faria da Silva (nathaliafsilva.ufv@gmail.com) on 2017-06-19T12:02:55Z No. of bitstreams: 1 texto completo.pdf: 1276596 bytes, checksum: e320e36eac8ecfc4d887e0c9f618329e (MD5) / Made available in DSpace on 2017-06-19T12:02:55Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1276596 bytes, checksum: e320e36eac8ecfc4d887e0c9f618329e (MD5) Previous issue date: 2005-04-29 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Por meio de um mecanismo denominado quorum sensing, diversas bactérias podem comunicar-se umas com as outras e coordenar a expressão gênica de acordo com a densidade populacional de forma semelhante aos organismos multicelulares. Este trabalho teve como objetivo investigar a produção de moléculas sinalizadoras de quorum, conhecidas como homoserinas lactonas aciladas (AHLs), por bactérias psicrotróficas proteolíticas isoladas de leite cru refrigerado. Verificou-se também se a atividade proteolítica de Pseudomonas fluorescens 07A é dependente da densidade populacional. Foram avaliados 53 isolados psicrotróficos proteolíticos e sete estirpes ATCC quanto à produção de AHL em meio sólido utilizando as bactérias Agrobacterium tumefaciens A136, Chromobacterium violaceum CV026 e Escherichia coli pSB403 como sistemas monitores ou sensores da presença de AHL. A produção de moléculas sinalizadoras foi freqüente entre os isolados psicrotróficos proteolíticos, constatando-se que, aproximadamente, 89 % das estirpes avaliadas foram produtoras de AHL. A extração de moléculas autoindutoras foi realizada em dois isolados, Serratia liquefaciens 016 e P. fluorescens 07A e, a presença de AHL nos extratos foi confirmada pelas estirpes monitoras C. violaceum CV026 e A. tumefaciens KYC55, respectivamente. A produção de AHL pelo isolado P. fluorescens 07A foi determinada em meio de cultivo à base de triptona suplementado com 0,25 % de cálcio (TYEP + CaCl 2 0,25 %) e em meio de constituição mínima (MMS), utilizando a estirpe monitora A. tumefaciens KYC55. Em meio TYEP + CaCl 2 0,25 % a produção de AHL(s) alcançou o máximo ao final da fase logarítmica, quando a população de P. fluorescens 07A foi da ordem de 10 9 UFC mL -1 . Esta mesma população resultou em uma concentração de AHL(s) cerca de três vezes menor no MMS. Os resultados indicaram que a produção de AHL pode estar sob controle de autoindução. O crescimento e a atividade proteolítica do isolado 07A foram avaliados em seis meios de cultivo. Não foi observada diferença no crescimento do isolado nos diferentes meios, exceto no MMS, onde a estirpe cresceu de forma mais lenta. Entretanto, a produção de proteases foi maior em meio TYEP + CaCl 2 0,25 % e em leite desnatado reconstituído (LDR 12 %). A detecção da atividade proteolítica só foi possível quando a cultura atingiu concentração populacional elevada em todos os meios avaliados, excetuando-se no meio MMS, quando a atividade proteolítica foi detectada em uma densidade populacional 10 vezes menor. Nos meios a base de triptona o pH aumentou para valores próximos a 8,5. Meios contendo íons Ca +2 apresentaram grande fluorescência ao final do período de incubação, indicando maior produção do sideróforo pioverdina. A adição de duas AHLs sintéticas não afetou o crescimento e a atividade proteolítica da estirpe P. fluorescens 07A em meio TYEP + CaCl 2 0,25 %. Quando comparada ao controle, a atividade proteolítica específica de P. fluorescens 07A não foi afetada significativamente, ao nível de 5% de probabilidade, pela suplementação do meio TYEP + CaCl 2 0,25 % com extrato de AHL obtido da própria estirpe. O quorum sensing pode não estar regulando a atividade proteolítica em P. fluorescens 07A. / In a process called quorum sensing, a range of bacterial cells communicate and coordinate the expression of multiple phenotypes according to cell density. This work aimed to evaluate the production of signaling molecules known as N-acyl homoserine lactone (AHL) by psychrotrophic proteolytic bacteria isolated from raw milk as well as to verify if the proteolytic activity of Pseudomonas fluorescens 07A is under the control of quorum sensing. Fifty three psychrotrophic isolates and seven ATCC cultures were screened for the production of AHL in agar systems using the monitor strains Agrobacterium tumefaciens A136, Chromobacterium violaceum CV026 and Escherichia coli pSB403. It was verified that almost 89 % of the psychrotrophic isolates tested elicited a positive response in at least one of the monitor strains of AHL. Signaling molecules were extracted from Serratia liquefaciens 016 and P. fluorescens 07A and the presence of AHL was detected with the monitor strains C. violaceum CV026 and A. tumefaciens KYC55, respectively. The production of AHL by the strain 07A was evaluated in a complex medium (TYEP + CaCl 2 0,25 %) and a defined medium (MMS). A. tumefaciens KYC55 was used to quantify AHL in this assay. In TYEP + CaCl 2 0,25 % the AHL concentration reached a maximum value at the end of xvthe stationary phase, when the population of P. fluorescens 07A was 10 9 CFU mL -1 . When MMS medium was used, a similar cell population was achieved, but the AHL concentration was three fold lower. The results indicated that AHL production by P. fluorescens 07A could be regulated by autoinduction. The growth and proteolytic activity of the P. fluorescens 07A were monitored in six different media. It was not observed difference in the specific growth rate of the strain in the media tested, except in MMS, where it grew slower. On the other hand, the protease activity was higher in the complex medium (TYEP + CaCl 2 0,25 %) and reconstituted skimmed milk (LDR 12 %). Proteolytic activity was only detected when the culture reached high population densities (10 8 UFC mL -1 ) in all media evaluated. In MMS, proteolytic activity was detected at lower population densities (10 7 UFC ml -1 ). An increase in pH values was observed during cultivation in media containing tryptone. The emission of fluorescence was intensified in media containing calcium. The addition of two synthetic AHLs did not affect the growth rates and the proteolytic activity of the strain 07A in TYEP + CaCl 2 0,25 %. Furthermore, the addition of AHL extracted from the culture did not increase the specific proteolytic activity in TYEP + CaCl 2 0,25 %. These results indicate that quorum sensing may not have a direct role in the regulation of protease production in P. fluorescens 07A.

Synonymous mutations have traditionally been thought to have no significant effect on fitness. However, a growing body of recent research has shown that this is not always the case. In an experimentally evolved population of Pseudomonas fluorescens grown in minimal glucose media, synonymous mutations arose in a glucose transport gene that resulted in beneficial fitness effects comparable to those of non-synonymous mutations. We found that the increase in fitness was a direct result of increased gene expression; however, the precise mechanism was unclear. Synonymous mutations have been shown to affect gene expression on transcriptional and translational levels through changes in mRNA secondary structure and codon usage. Our study investigates the underlying mechanisms in which these evolved synonymous mutations lead to increased gene expression. In addition to the evolved mutations, we have a library of 42 strains with single synonymous mutations within the glucose transport gene and found a positive correlation between fitness and gene expression. To determine whether these mutations affect transcript levels, translational efficiency or a combination of both, we systematically incorporated transcriptional and translational fusions of a yellow fluorescent protein within the glucose transport operon. We found that the evolved mutations predominantly act on the level of transcription and have strong polar downstream effects. Additionally, through manipulation of the local genetic sequence, we investigated the specific molecular requirements necessary for the increased expression. We found that for one of our evolved synonymous mutants, mRNA secondary structure does not play an essential role, but we speculate that the mutation may strengthen a weak internal promoter sequence to confer its increased expression. Our study provides evidence of the adaptive mechanisms of beneficial synonymous mutations in an experimentally evolved setting.

Cyanide utilization in Pseudomonas fluorescens NCIMB 11764 occurs via oxidative conversion to carbon dioxide and ammonia, the latter satisfying the nitrogen requirement. Substrate attack is initiated by an enzyme referred to as cyanide oxygenase (CNO), previously shown to require components in both high (H) (>30 kDa) and low (L) (<10 kDa) molecular weight cell fractions. In this study, tetrahydrobiopterin (H4biopterin) was identified as a cofactor in fraction L, thus making CNO appear as a pterin- dependent hydroxylase. CNO was purified 150-fold (specific activity 0.9 U/mg) and quantitatively converted cyanide to formate and ammonia as reaction products. When coupled with formate dehydrogenase, the complete enzymatic system for cyanide oxidation to carbon dioxide and ammonia was reconstituted. CNO was found to be an aggregate of known enzymes that included NADH oxidase (Nox), NADH peroxidase (Npx), cyanide dihydratase (CynD) and carbonic anhydrase (CA). A complex multi-step reaction mechanism is proposed in which Nox generates hydrogen peroxide which in turn is utilized by Npx to catalyze the oxygenation of cyanide to formamide accompanied by the consumption of one and two molar equivalents of oxygen and NADH, respectively. The further hydrolysis of formamide to ammonia and formate is thought to be mediated by CynD. The role of H4biopterin and of the enzyme CA in the proposed process remains unclear, but the involvement of each in reactive oxygen and radical chemistry is consistent with the proposed formation of such species in the catalytic process. H4biopterin may additionally serve as a protein stabilizing agent along with a protein co-purifying with CynD identified as elongation factor Tu, a known chaperone. At least two of the CNO components (Nox and CynD) are complex oligomeric proteins whose apparent association with Npx and CA appears to be favored in bacterial cells induced with cyanide allowing their purification in toto as a multiprotein enzyme complex.

No description available.

Cyanide is a well known toxicant that arises in the environment from both biological and industrial sources. Bacteria have evolved novel coping mechanisms for cyanide and function as principal agents in the biosphere for cyanide recycling. Some bacteria exhibit the unusual ability of growing on cyanide as the sole nitrogen source. One such organism is Pseudomonas fluorescens NCIMB 11764 (Pf11764) which employs a novel oxidative mechanism for detoxifying and assimilating cyanide. A unique complex of enzymes referred to as cyanide oxygenase (CNO) is responsible for this ability converting cyanide to ammonia which is then assimilated. Because one component of the four member CNO complex was previously shown to act on cyanide independent of the other members, its characterization was sought as a means of gaining a better understanding of the overall catalytic mechanism of the complex. Preliminary studies suggested that the enzyme belonged to a subset of nitrilase enzymes known as cyanide dihydratases (CynD), however, a cynD-like gene in Pf11764 could not be detected by PCR. Instead, a separate nitrilase (Nit) linked to cyanide metabolism was detected. The corresponding nit gene was shown to be one of a conserved set of nit genes traced to a unique cluster in bacteria known as Nit1C. To determine whether the previously described CynD enzyme was instead Nit, efforts were undertaken to isolate the enzyme. This was pursued by cloning and expressing the recombinant enzyme and by attempting to isolate the native enzyme. This thesis is concerned with the latter activity and describes the purification of a Nit-like cyanide-degrading nitrilase (NitCC) from Pf11764 to ~95% homogeneity. Purification was greatly facilitated by the discovery that fumaronitrile, as opposed to cyanide, was the preferred substrate for the enzyme (20 versus 1 U/mg protein, respectively). While cyanide was less effective as a substrate, the specificity for cyanide far outweighed that (10,000 fold) of the recombinant enzyme (NitPG) implying that the native NitCC protein purified in this work is different from that of the cloned recombinant. Further evidence of this was provided by molecular studies indicating that the two proteins differ in mass (34.5 and 38 kDa, respectively) and amino acid sequence. In summary, two different Nit enzymes are encoded by Pf11764. While the two share greater than 50% amino acid sequence identity, the results suggest that the native NitCC enzyme purified in this work functions better as a cyanide-degrading nitrilase and is one of four enzyme components comprising CNO required for Pf11764 cyanide assimilation.

Pseudomonas fluorescens does not appear to regulate the enzymes of de novo pyrimidine biosynthesis at the level of gene expression. Little or no apparent repression of pyr gene expression is observed upon addition of exogenous pyrimidines to the growth medium. The Escherichia coli pyrBI genes for aspartate transcarbamoylase (ATCase) were sized down and cloned into the broad host range plasmid, pKT230. Upon introduction into a P.fluorescenspyrB mutant strain, ATCase showed repression in response to exogenously fed pyrimidine compounds. Thus, it was possible to bring about changes in pyrimidine nucleotide pool levels and in transcriptional regulation of gene expression at the same time.

Évolution expérimentale aux limites de l'extinction : Le cas de Pseudomonas fluorescens soumise au stress. Les stress environnementaux : ces perturbations d'origine biotiques ou abiotiques des conditions de vie qui ont un impact sur les populations par l'altération des capacités de reproduction et/ou de survie des organismes, peuvent parfois mener une espèce à l'extinction si celle-ci n'est pas en mesure de s'adapter suffisamment rapidement. Avec l'augmentation de l'impact des activités humaines, le taux d'extinction des espèces est aujourd'hui estimé être de plusieurs ordres de grandeur au dessus du taux d'extinction basal. Il est donc important de comprendre les facteurs écologiques et évolutifs, à l'échelle de l'espèce comme de la communauté, qui déterminent la survie ou l'extinction d'une espèce soumise à un stress sévère.Au cours de cette thèse, nous utiliserons les outils de l'évolution expérimentale avec la bactérie Pseudomonas fluorescens soumise à un stress antibiotique, ainsi que des outils théoriques, pour étudier les facteurs déterminants les conditions d'un sauvetage évolutif : événement d'évolution rapide d'une population en situation d'effondrement démographique sous l'effet d'un stress létal. Nous étudierons aussi le rôle d'un stress plus modérés : une carence en ressource, sur deux aspects de la structure des communautés liés à la stabilité de ces dernières face aux perturbations environnementales : La topologie d'un réseau trophique bactérie-phage, ainsi que la distribution des tailles de populations, décrite par la loi de Taylor, pour des populations bactériennes en mono-culture ou en compétition sur un gradient de ressource. Nos travaux ont permis de mieux comprendre le sauvetage évolutif, en montrant notamment le rôle déterminant de la taille des populations et de leur diversité génétique initiale dans la capacité d'adaptation à un stress létal. Mais aussi en proposant une meilleure description des dynamiques de populations typiques de cette situation. Nous avons aussi montré la capacité d'une limitation des ressources à altérer la structure des réseaux trophiques et ainsi leur stabilité face aux perturbations. / Experimental Evolution at the Edge of Extinction, The Case of Pseudomonas fluorescens in Stressful Environments.Environmental stresses : the biotic or abiotic perturbations of life conditions which have an impact on populations through impaired organism's ability to survive and/or reproduce, can sometimes result in species extinction if rapid evolutionary adaptation doesn't occur. With the increasing impact of human activities, the rate of species extinction is now estimated to be several orders of magnitudes above the background rate. It is therefore crucial to understand the ecological and evolutionary factors, at species and community levels, which determine the survival or extinction of species exposed to severe stresses. All along this thesis, we will use experimental evolution tools with the bacterium Pseudomonas fluorescens exposed to antibiotic stress, as well as theoretical tools, to study the factors driving evolutionary rescue : the rapid evolutionary adaptation occurring in populations experiencing demographic collapse under a lethal stress. Then we will study how a moderate stress (low resource availability) drives different aspects of communities structure related to their stability against environmental perturbations : The topology of a bacteria-bacteriophage trophic network, and the distribution of population sizes along a resource gradient, described by Taylor's law, for bacterial populations either in mono-culture or in competition. Our results led to a better understanding of evolutionary rescues. In particular, we show the crucial role of initial population size and genetic diversity in the ability to evolve adaptation to an initially lethal stress. And we refined the description of populations dynamics in such cases. We show also how resource limitation can disturb trophic network structure, resulting in a lower stability against environmental perturbations.