Recentemente, o bis-(3\',5\')-di-guanosina monofosfato cíclico (c-di-GMP) surgiu como uma importante molécula sinalizadora nas bactérias. Essa molécula foi identificada como uma das responsáveis pelo controle do comportamento bacteriano e está relacionada com a patogenicidade e a adaptação de diversas bactérias, coordenando a expressão de genes envolvidos com virulência, motilidade e formação de biofilme. O mecanismo pelo qual c-diGMP atua vem sendo motivo de estudo de vários grupos de pesquisa nos últimos anos. Já foi demonstrado o papel dessa molécula em diferentes etapas do controle da expressão gênica. Acredita-se que a manipulação dos níveis de c-di-GMP pode ser uma nova abordagem terapêutica contra bactérias patogênicas. Pseudomonas aeruginosa é uma proteobactéria do grupo gama, que atua como um patógeno oportunista, causando infecções em pacientes imunocomprometidos, sendo o maior causador de infecções crônicas em pacientes portadores de fibrose cística. O genoma de P. aeruginosa PA14 apresenta vários genes que codificam proteínas envolvidas no metabolismo e/ou ligação de c-di-GMP, o que pode indicar um amplo papel regulatório deste nucleotídeo nessa bactéria. Uma associação infundada entre níveis elevados de c-di-GMP e a resistência aos antibióticos é geralmente assumida, já que altos níveis de c-di-GMP levam à formação de biofilme, que é comprovadamente um modo de crescimento mais resistente. Nesse trabalho, utilizando uma abordagem proteômica, mostramos que Pseudomonas aeruginosa PA14 regula a expressão de cinco porinas em resposta a variações nos níveis de c-di-GMP, independentemente dos níveis de mRNA. Uma dessas porinas, OprD, é responsável pela entrada do antibiótico β-lactâmico imipenem na célula e é menos abundante em condições de alto c-di-GMP. Também demonstramos que linhagens com altos níveis de c-di-GMP apresentam uma vantagem competitiva de crescimento em relação a linhagens com níveis mais baixo de c-di-GMP quando crescidas em meio contendo imipenem. Em contraste, observamos que células planctônicas com elevados níveis c-di-GMP são mais sensíveis a tobramicina. Em conjunto, estes resultados mostram que c-di-GMP pode regular a resistência a antibióticos em sentidos opostos, e independentemente do crescimento em biofilme / Following the genomic era, a large number of genes coding for enzymes predicted to synthesize and degrade 3\'-5\'-cyclic diguanylic acid (c-di-GMP) was found in most bacterial genomes and this dinucleotide emerged as an important intracellular signal molecule controlling bacterial behavior. Diverse molecular mechanisms have been described as targets for c-di-GMP, but several questions remain to be addressed. An association between high c-di-GMP levels and antibiotic resistance is largely assumed, since high c-di-GMP upregulates biofilm formation and the biofilm mode of growth leads to enhanced antibiotic resistance; however, a clear understanding of this correlation is missing. Pseudomonas aeruginosa is a versatile gamma-proteobacterium that behaves as an opportunistic pathogen to a broad range of hosts. The ability of P. aeruginosa to form biofilms contributes to its virulence and adaptation to different environments. The P. aeruginosa PA14 genome presents several genes encoding proteins involved in metabolism or binding to c-di-GMP, which may indicate a wide regulatory role of this nucleotide in this bacterium. Here, using a proteomic approach, we show that Pseudomonas aeruginosa PA14 regulates the amount of five porins in response to c-di-GMP levels, irrespective of their mRNA levels. One of these porins is OprD, decreased in high c-di-GMP conditions, which is responsible for the uptake of the β-lactam antibiotic imipenem. We also demonstrate that this difference leads strains with high c-di-GMP to be more resistant to imipenem even when growing as planktonic cells, giving them a competitive advantage over cells with low c-di-GMP. Contrastingly, we found that planktonic cells with high c-di-GMP levels are more sensitive to aminoglycosides antibiotics. Together, these findings show that c-di-GMP levels can regulate the antibiotic resistance to different drugs in opposite ways and irrespective of a biofilm mode of growth.

Für die E. coli K12 Biofilmbildung ist die Expression des Masterregulators CsgD essentiell. Dies erfordert das Signalmolekül c-di-GMP, dessen Auf- und Abbau durch 12 Diguanylatzyklasen (DGCs mit GGDEF-Domänen) und 13 Phosphodiesterasen (PDEs mit EAL-Domänen) erfolgt. DgcE ist mit einer MASE1-umfassenden Transmembranregion (TM), drei PAS-, einer GGDEF- und einer degenerierten EAL-Domäne die strukturell komplexeste DGC und notwendig für die Biofilmbildung. Diese Arbeit zeigt, dass die Aktivität von DgcE einer hoch komplexen Regulation unterliegt. Einzelnen DgcE-Domänen konnten aktivierende bzw. inhibierende Rollen hinsichtlich der Biofilmmatrixsynthese zugeordnet werden. Die Biofilmbildung hängt von DgcE-produziertem c-di-GMP ab, wobei die DgcE-Dimerisierung v.a. durch die PAS-Region vermittelt wird. Die EAL-Domäne wirkt einer aktiven DgcE-Form entgegen. Für die DgcE-vermittelte Matrixproduktion sind die GTPase YjdA und sein Partnerprotein YjcZ nötig. Über Interaktionen mit YjcZ und der TM von DgcE vermittelt YjdA eine Komplexbildung. Die Interaktion von YjdA und DgcE sowie die Matrixproduktion hängen von der GTPase-Aktivität von YjdA ab. GTP wird daher als intrazelluläres Signal vorgeschlagen, das die Aktivierung von DgcE durch YjdA/YjcZ reguliert. Die MASE1-umfassende TM agiert als Zentrale der Signalintegration. Einerseits ist sie nötig für die DgcE-Aktivität und andererseits ist sie an einem massiven Abbau von DgcE beteiligt. Zudem wurden neu identifizierte Curli-regulierende Gene (rbsK, rbsR, ydcI, yieP, puuR) untersucht, wobei keines über das PdeR/DgcM/MlrA-Modul in die c-di-GMP-vermittelte CsgD-Expression eingreift. Flagellare Verknotungen in der unteren Schicht von E. coli Makrokolonien tragen zur Morphogenese dieser Makrokolonien bei. Diese Arbeit zeigt, dass Flagellenverknotungen zu einer verminderten Expression der Master-PDE PdeH beitragen, wodurch vermutlich die zelluläre c-di-GMP-Konzentration steigt und somit die Biofilmbildung begünstigt wird. / Biofilm formation of E. coli K12 requires the expression of the biofilm master regulator CsgD. This process depends on the signaling molecule c-di-GMP, which is synthesized by 12 diguanylate cyclases (DGCs with GGDEF domains) and degraded by 13 phosphodiesterases (PDEs with EAL domains). DgcE is the most complex DGC with a MASE1-containing transmembrane region (TM), three PAS, a GGDEF and a degenerate EAL domain, and it is essential for biofilm formation. This work shows that the regulation of the DgcE activity is highly complex. It was possible to assign activating and inhibitory roles to single domains of DgcE with regard to the expression of biofilm matrix components. C-di-GMP produced by DgcE is necessary for biofilm matrix production. The dimerization of DgcE is mainly mediated by the PAS region, whereas the EAL domain counteracts an active form of DgcE. DgcE-mediated matrix synthesis requires the activating signal input of the GTPase YjdA and its partner protein YjcZ. DgcE, YjdA and YjcZ form a protein complex in which YjdA directly interacts with YjcZ and the TM of DgcE. The interaction between DgcE and YjdA as well as the matrix expression depend on the GTPase activity of YjdA. Thus, it is proposed that GTP serves as an intracellular signal regulating the activation of DgcE by YjdA/YjcZ. The MASE1-containing TM proved to be a central hub for signal integration. It is both required for DgcE activity and for a massive degradation of DgcE. Furthermore, newly discovered curli-regulating genes (rbsK, rbsR, ydcI, yieP, puuR) have been analyzed. None of those gene products act on CsgD expression via the PdeR/DgcM/MlrA module. Flagellar entangling within the bottom layer of E. coli macrocolonies determines morphogenesis of macrocolonies. The data presented here suggest that the master PDE PdeH is somehow down-regulated by flagellar entangling, which probably results in a higher cellular c-di-GMP concentration, thereby promoting biofilm formation.

Die Entwicklung des grampositiven Bodenbakteriums Streptomyces ist in einem komplexen Lebenszyklus koordiniert, bestehend aus drei Stufen: vegetativem Hyphenwachstum, Luftmycelbildung und Sporulation. C-di-GMP kontrolliert die Enwicklung über zwei Effektorproteine: dem Masterregulator BldD und dem Anti-Sigmafaktor RsiG. In dieser Arbeit konnte gezeigt werden, dass das membranständige GGDEF-EAL Protein CdgC eine wichtige aktive Diguanylatzyklase (DGC) in S. venezuelae ist. Chromosomale Deletion von cdgC führte zu einer flachen, gräulichen Koloniemorphologie mit radialen Stegen und hydrophiler Oberfläche sowie zu frühzeitiger Sporulation ohne Lufthyphenbildung. Phänotypische Analysen zeigten, dass die DGC-Aktivität von CdgC essentiell ist für dessen biologische Rolle und deuten auf einen zusätzlichen Protein-spezifischen morphologischen Effekt von CdgC hin. CdgC-FLAG akkumuliert im Laufe des Lebenszyklus und scheint BldD-abhängig über eine c-di-GMP vermittelte Feedbackschleife reguliert zu werden. Frühere RNA-seq Daten, verifiziert für repräsentative Gene mittels qRT-PCR, deuten eine differentielle Expression der Bestandteile des hydrophoben Mantels als Ursache der Lufthyphendefizienz an. Konfokalmikroskopische Aufnahmen des bakteriellen Tubulin-Homologons FtsZ deuten einen c-di-GMP-sensitiven Einfluss von CdgC auf die Koordination der Zellteilung an. Zudem konnte nachgewiesen werden, dass CdgC mit sich selbst sowie drei potentiellen Membranproteinen interagiert. Demnach trägt CdgC zur Koordination von Zellteilungs- und hydrophoben Zelloberflächenproteinen bei und beeinflusst damit c-di-GMP-abhängig den Zeitpunkt der Sporenbildung. Insgesamt führt diese Studie CdgC als GGDEF-EAL-Tandemprotein mit spezifischem Knockout- Phänotyp ein, der von seiner DGC-Aktivität sowie seinem Membrananker bestimmt wird. Zudem ist CdgC, als Reaktion auf eine noch unbekannte Signalübertragungskaskade, an der Koordinierung von Zeitpunkt und Verlauf der Sporulation ausschlaggebend beteiligt. / The proliferation of Gram-positive soil bacteria Streptomyces is temporally and genetically coordinated with a complex developmental life cycle, including three main stages of differentiation: vegetative hyphal growth, formation of aerial mycelium and sporulation. The key factor of Streptomyces developmental control is c-di-GMP with to-date two identified effector proteins: the master regulator BldD and the anti-sigma factor RsiG. In this thesis, the membrane-associated GGDEF-EAL protein CdgC, was identified as a major active diguanylate cyclase (DGC) in S. venezuelae. Deletion of cdgC results in the unique flat gray colony morphology with radial wrinkles and a hydrophilic surface, that shows enhanced sporulation without forming aerial hyphae. Phenotypic analyses suggest, that the DGC activity is essential for its biological role, but hint to an additional protein specific role. The protein levels of CdgC-FLAG were found to accumulate during the life cycle of S. venezuelae. Further investigation of CdgC-FLAG in a strain carrying a DNA-binding deficient BldD_D116A allele indicated, that BldD represses the expression of CdgC in a regulatory feedback loop along with the DGCs CdgA, CdgB and CdgE. RNA‐sequencing data indicated that reduced expression levels of the major compounds of the hydrophobic sheath result in the initiation of sporulation out of the vegetative mycelium and were verified for representative examples via qRT-PCR. Confocal microscopic imaging of the bacterial tubulin homolog FtsZ indicated a contribution of CdgC via its DGC activity in coordination of the cell division. In addition, BTH screenings revealed self-interaction and identified three membrane associated interaction partners. In conclusion, this study introduces the GGDEF-EAL tandem protein CdgC, whose specific knockout phenotype is governed by its DGC activity and membrane association. CdgC seems to drive timing and mode of sporulation in response to an unknown signal to a major extend.

Streptomyceten weisen einen komplexen Lebenszyklus auf, dessen Verlauf durch den sekundären Botenstoff Bis-(3´- 5´)-zyklisches dimeres Guanosinmonophosphat (c-di-GMP) und die c-di-GMP-Effektorproteine BldD und RsiG reguliert wird. Der Auf- bzw. Abbau von c-di-GMP wird von Diguanylatzyklasen (DGC) mit GGDEF-Domänen bzw. Phosphodiesterasen (PDE) mit EAL- oder HD-GYP-Domänen katalysiert. In S. venezuelae, einem Modellorganismus der Streptomyceten, konnten zehn potenziell c-di-GMP metabolisierende Enzyme identifiziert werden, von welchen mit RmdA und RmdB zwei GGDEF-EAL-Tandem-Proteine im Fokus dieser Arbeit stehen. Die chromosomale Deletion der für RmdA und RmdB kodierenden Gene führt zu einer ausgeprägten Verzögerung der Entwicklung in S. venezuelae. Mit Hilfe chromosomaler Mutationen konnten die EAL-Motive der EAL-Domänen als essenziell für die in vivo Funktion beider Proteine identifiziert werden. Beide Proteine zeigen in vitro PDE-Aktivität und RmdA konnte als bifunktionales Enzym charakterisiert werden, da es in vitro auch DGC-Aktivität aufweist. Mittels Nukleotidextraktionen konnte RmdB als Haupt-PDE in S. venezuelae identifiziert werden, welche über den gesamten Entwicklungsverlauf für den Abbau von c-di-GMP verantwortlich ist. Aber auch RmdA hat während des Übergangs von der vegetativen zur reproduktiven Wachstumsphase Einfluss auf die globale zelluläre c-di-GMP Konzentration. Durchgeführte Transkriptomanalysen und qRT-PCR-Experimente ergaben, dass in den Deletionsmutanten die Expression einiger wichtiger entwicklungsspezifischer Gene im Vergleich zum Wildtyp herunterreguliert ist. Dies ist vermutlich auf die erhöhten c-di-GMP Konzentrationen in den Deletionsmutanten zurückzuführen, wodurch die Aktivität der c-di-GMP-Effektorproteine BldD und RsiG beeinflusst wird und die verzögerte Entwicklung der Deletionsmutanten erklärt werden kann. Weiterhin konnte gezeigt werden, dass RmdB mit dem Sigmafaktor der Sporulation, WhiG, interagieren kann. / Streptomycetes show a complex life cycle. The transition between the different developmental stages is regulated by the secondary messenger bis- (3´- 5´) -cyclic dimeric guanosine monophosphate (c-di-GMP) and the c-di-GMP effector proteins BldD and RsiG. c-di-GMP is synthesized by diguanylate cyclases (DGCs) with GGDEF domains, and its degradation is catalyzed by phosphodiesterases (PDE) with EAL or HD-GYP domains. In S. venezuelae, the Streptomyces strain which was used as a model organism in this work, there are ten potentially c-di-GMP metabolizing enzymes, of which two GGDEF-EAL tandem proteins, RmdA and RmdB, are the focus of this work. The deletion of the genes coding for RmdA and RmdB leads to a pronounced developmental delay in S. venezuelae. With the help of chromosomal mutations, the EAL motif was identified as essential for the in vivo function of RmdA and RmdB. Furthermore, both proteins were characterized in vitro as active PDEs and RmdA as a bifunctional enzyme, which also showed DGC activity. RmdB was identified as the master PDE in S. venezuelae by means of nucleotide extraction and is responsible for the hydrolysis of c-di-GMP over the course of development investigated. Also RmdA has an influence on the global cellular c-di-GMP concentration during the transition from the vegetative to the reproductive growth phase. A transcriptome analysis, qRT-PCR experiments and related follow-up experiments showed that the deletion of rmdA and rmdB leads to a differential expression of genes which code for important development-specific factors and regulators. This is presumably due to the increased c-di-GMP concentrations in the deletion mutants, with the c-di-GMP effector proteins BldD and RsiG delaying the transition to the next growth phase. Furthermore, it could be shown that RmdB can interact with the sigma factor of sporulation, WhiG.

Malgré la découverte du c-di-GMP en 1987, ce n’est que durant la dernière décennie que l’importance de ce messager secondaire dans la régulation des phénotypes bactériens a été exposée. Synthétisé par des diguanylate cyclases (DGC) et dégradé par des phosphodiestérases spécifiques (PDE), le c-di-GMP est prédit pour être un messager secondaire très répandu chez les bactéries et pratiquement exclusif à celles-ci. Le c-di-GMP est particulièrement reconnu pour son rôle dans la transition des bactéries motiles et planctoniques vers la formation de biofilm chez les bactéries à Gram négatif telles qu’Escherichia coli, Pseudomonas aeruginosa et Vibrio cholerae. De plus, le c-di-GMP est impliqué dans la régulation de l’expression de certains facteurs de virulence chez certaines bactéries. Ainsi, il est possible de révéler les mécanismes de régulation de certains phénotypes importants par l’étude de la signalisation à c-di-GMP dans une bactérie donnée. Clostridium difficile est une bactérie pathogène causant des diarrhées nosocomiales, des colites et pouvant causer des décès chez l’Homme. Les phénotypes impliqués dans la pathogenèse de C. difficile et leur régulation demeurent en grande partie méconnus. Le génome de C. difficile 630 était prédit être capable de coder pour 37 DGC et PDE putatives, un nombre en apparence élevé pour une bactérie à Gram positif. L’objectif global de mon doctorat était de déterminer si la signalisation à c-di-GMP était fonctionnelle chez C. difficile puis de déterminer le rôle du c-di-GMP chez cette bactérie. Dans un premier projet, mes travaux de doctorat ont permis de démontrer que la majorité des 37 DCG et PDE putatives chez C. difficile 630 sont fonctionnelles. Les 31 DCG et PDE les plus conservées dans les différentes souches de C. difficile ont été exprimées dans V. cholerae afin d’évaluer indirectement leur capacité de synthèse et de dégradation du c-di-GMP en mesurant leur impact sur motilité et la formation de biofilm de V. cholerae. La surexpression d’une DGC chez V. cholerae réduit la motilité par flagelle et augmente la formation de biofilm, alors que l’inverse est observé lors de la surexpression d’une PDE. De plus, l’activité d’une DCG, CD1420 (renommée DccA, CD630_14200), et une PDE, CD0757 (renommée CD630_07570) a été démontrée plus explicitement par des essais enzymatiques in vitro. Ainsi, ce projet a exposé l’important potentiel de la signalisation à c-di-GMP chez C. difficile, jusqu’alors étudiée presque exclusivement chez les bactéries à Gram négatif. Dans un deuxième projet, mes travaux de doctorat ont permis de démontrer le rôle des pili de type IV (T4P) dans l’agrégation de C. difficile et la régulation de leur expression par un riborégulateur à c-di-GMP. Les riborégulateurs sont des structures ARN situées dans la région 5’UTR des gènes capables de réguler l’expression des gènes en aval en fonction de la liaison d’un métabolite spécifique. Parmi les 16 riborégulateurs à c-di-GMP prédits dans le génome de C. difficile 630, le riborégulateur c-di-GMP-II Cdi2_4 est situé en amont du locus principal de synthèse de T4P. Mes travaux ont permis de montrer que l’augmentation de la concentration de c-di-GMP intracellulaire se traduit par une augmentation de l’expression des gènes de T4P, la formation de T4P à la surface des cellules et l’agrégation dépendante des T4P. De plus, le mécanisme de régulation du riborégulateur Cdi2_4 a été démontré in vitro. La liaison du c-di-GMP au riborégulateur Cdi2_4 prévient la formation d’un terminateur transcriptionnel et favorise ainsi la transcription des gènes de T4P en aval. Depuis la mise en évidence de la signalisation à c-di-GMP chez C. difficile dans la première partie de mon doctorat, un certain nombre de phénotypes régulés par c-di-GMP chez cette bactérie ont pu être déterminés ou prédits. Notamment, le c-di-GMP inhibe la transcription des gènes des flagelles en se liant au riborégulateur c-di-GMP-I Cd1 en amont et inhibe indirectement la production des toxines TcdA et TcdB. La démonstration de l’effet positif du c-di-GMP sur l’agrégation des cellules via les T4P, dans la deuxième partie de mon doctorat, contribue à notre compréhension de la signalisation à c-di-GMP chez C. difficile. Il apparait que le c-di-GMP inhibe la motilité et favorise la formation de structures pluricellulaires chez C. difficile à l’instar de plusieurs bactéries, néanmoins par des mécanismes de régulation distincts.

Periodontal disease is a progressive inflammatory condition that is characterized by the reabsorption of alveolar bone, the destruction of connective tissue, and edentulism. It is caused by a dysbiosis in the oral microbiome as a result of a shift from a Gram-positive aerobic bacterial population, to one that becomes more Gram-negative and anaerobic. Treponema denticola is thought to drive this diseased state based on its role as a keystone periopathogen. A major component of T.denticola’s invasiveness is its motility, which allows the spirochete to penetrate and disseminate through tissues. This motility, which has been seen to be crucial to the invasiveness in other spirochetes through deletion studies, is often regulated by the second messenger, c-di-GMP. In this study, biochemical and biophysical assays were utilized to determine that the predicted diguanylate cyclase TDE0125 converts GTP to c-di-GMP. This elucidates further function of the c-di-GMP regulatory network in T. denticola.

Bacteria living in soil and aquatic habitats rapidly adapt to changes in physico-chemical parameters that influence their energy status and thus their ability to proliferate and survive. One immediate survival strategy is to relocate to more metabolically optimal environments. To aid their movement through gradients (a process called taxis), many bacteria use whip like flagella organelles. Soil-dwelling Pseudomonas putida possesses a polar bundle of flagella that propel the bacterium forward in directed swimming motility. P. putida strains are generally fast growing, have a broad metabolic capacity, and are resistant to many harmful substances – qualities that make them interesting for an array of industrial and biotechnological application. This thesis identifies some of the factors that are involved in controlling the flagella driven motility of P. putida. In the first part of the thesis, I present evidence that P. putida displays energy-taxis towards metabolisable substrates and that the surface located Aer2 receptor (named after its similarities to the Escherichia coli Aer receptor) is responsible for detecting the changes in energy-status and oxygen-gradients that underlie this response. Aer2 is expressed simultaneously with the flagella needed for taxis responses and its expression is ensured during nutrient scares conditions through the global transcriptional regulators ppGpp and DksA. In addition to Aer2, P. putida possesses two more Aer-like receptors (Aer1 and Aer3) that are differentially expressed. Like Aer2, Aer1 and Aer3 co-localize to one cell pole. Although the signals to which Aer1 and Aer3 respond are unknown, analysis of Aer1 uncovered a role in motility control for a protein encoded within the same operon. This protein, called PP2258, instigated the work described in the second part of my thesis on the involvement of the second messenger c-di-GMP in regulation of P. putida motility. Genetic dissection of the catalytic activities of PP2258 revealed that it has the unusual capacity to both synthesize and degrade c-di-GMP. Coupling of the c-di-GMP signal originating from PP2258 to motility control was traced to the c-di-GMP binding properties of the protein PP4397. In the last part of the thesis, I present possible mechanisms for how these different components might interact to create a signal transduction cascade – from the surface located Aer1 receptor to PP2258 and the c-di-GMP responsive PP4397, and from there to the flagella motors – to ultimately determine flagella performance and the motility status of P. putida.

Evaluating aerodynamic noise from aircraft engines is a design stage process, so that it conform to regulations at airports. Aerodynamic noise is also a principal source of structural vibration and internal noise in short/vertical take off and landing and rocket launches. Acoustic loads may be critical for the proper functioning of electronic and mechanical components. It is imperative to have tools with capability to predict noise generation from turbulent flows. Understanding the mechanism of noise generation is essential in identifying methods for noise reduction. Lighthill (1952) and Lighthill (1954) provided the first explanation for the mechanism of aerodynamic noise generation and a procedure to estimate the radiated sound field. Many such procedures, known as acoustic analogies are used for estimating the radiated sound field in terms of the turbulent fluid flow properties. In these methods, the governing equations of the fluid flow are rearranged into two parts, the acoustic sources and the propagation terms. The noise source terms and propagation terms are different in different approaches. A good description of the turbulent flow field and the noise sources is required to understand the mechanism of noise generation. Computational aeroacoustics (CAA) tools are used to calculate the radiated far field noise. The inputs to the CAA tools are results from CFD simulations which provide details of the turbulent flow field and noise sources. Reynolds-Averaged Navier Stokes (RANS) solutions can be used as inputs to CAA tools which require only time-averaged mean quantities. The output of such tools will also be mean quantities. While complete unsteady turbulent flow details can be obtained from Direct Numerical Simulation (DNS), the computation is limited to low or moderate Reynolds number flows. Large eddy simulations (LES) provide accurate description for the dynamics of a range of large scales. Most of the kinetic energy in a turbulent flow is accounted by the large-scale structures. It is also the large-scale structures which accounts for the maximum contribution towards the radiated sound field. The results from LES can be used as an input to a suitable CAA tool to calculate the sound field. Numerical prediction of turbulent flow field, the acoustic sources and the radiated sound field is at the focus of this study. LES based on explicit filtering method is used for the simulations. The method uses a low-pass compact filter to account for the sub-grid scale effects. A one-parameter fourth-order compact filter scheme from Lele (1992) is used for this purpose. LES has been carried out for four different flow situations: (i) round jet (ii) plane jet (iii) impinging round jet and (iv) impinging plane jet. LES has been used to calculate the unsteady flow evolution of these cases and the Lighthill’s acoustic sources. A compact difference scheme proposed by Hixon & Turkel (1998) which involves only bi-diagonal matrices are used for evaluating spatial derivatives. The scheme provides similar spectral resolution as standard tridiagonal compact schemes for the first spatial derivatives. The scheme is computationally less intensive as it involves only bi-diagonal matrices. Also, the scheme employs only a two-point stencil. To calculate the radiated sound field, the Helmholtz equation is solved using the Green’s function approach, in the form of the Kirchhoff-Helmholtz integral. The integral is performed over a surface which is present entirely in the linear region and covers the volume where acoustic sources are present. The time series data of pressure and the normal component of the pressure gradient on the surface are obtained from the CFD results. The Fourier transforms of the time series of pressure and pressure gradient are then calculated and are used as input for the Kirchhoff-Helmholtz integral. The flow evolution for free jets is characterised by the growth of the instability waves in the shear layer which then rolls up into large vortices. These large vortical structures then break down into smaller ones in a cascade which are convected downstream with the flow. The rms values of the Lighthill’s acoustic sources showed that the sources are located mainly at regions immediately downstream of jet break down. This corresponds to the large scale structures at break down. The radiated sound field from free jets contains two components of noise from the large scales and from the small scales. The large structures are the dominant source for the radiated sound field. The contribution from the large structures is directional, mainly at small angles to the downstream direction. To account for the difference in jet core length, the far field SPL are calculated at points suitably shifted based on the jet core length. The peak value for the radiated sound field occurs between 30°and 35°as reported in literature. Convection of acoustic sources causes the radiated sound field to be altered due to Doppler effect. Lighthills sources along the shear layer were examined in the form of (x, t) plots and phase velocity pattern in (ω, k) plots to analyse for their convective speeds. These revealed that there is no unique convective speeds for the acoustic sources. The median convective velocity Uc of the acoustic sources in the shear layer is proportional to the jet velocity Uj at the center of the nozzle as Uc ≈ 0.6Uj. Simulations of the round jet at Mach number 0.9 were used for validating the LES approach. Five different cases of the round jet were used to understand the effect of Reynolds number and inflow perturbation on the flow, acoustic sources and the radiated sound field. Simulations were carried out for an Euler and LES at Reynolds number 3600 and 88000 at two different inflow perturbations. The LES results for the mean flow field, turbulence profiles and SPL directivity were compared with DNS of Freund (2001) and experimental data available in literature. The LES results showed that an increase in inflow forcing and higher Reynolds number caused the jet core length to reduce. The turbulent energy spectra showed that the energy content in smaller scale is higher for higher Reynolds number. LES of plane jets were carried out for two different cases, one with a co-flow and one without co-flow. LES of plane jets were carried out to understand the effect of co-flow on the sound field. The plane jets were of Mach number 0.5 and Reynolds number of 3000 based on center-line velocity excess at the nozzle. This is similar to the DNS by Stanley et al. (2002). It was identified that the co-flow leads to a reduction in turbulence levels. This was also corroborated by the turbulent energy spectrum plots. The far field radiation for the case without co-flow is higher over all angles. The contribution from the low frequencies is directional, mainly towards the downstream direction. The range of dominant convective velocities of the acoustic sources were different along shear layers and center-line. The plane jet results were also used to bring out a qualitative comparison of flow and the radiation characteristics with round jets. For the round jet, the center-line velocity decays linearly with the stream-wise distance. In the plane jet case, it is the square of the center-line velocity excess which decays linearly with the stream-wise distance. The turbulence levels at any section scales with the center-line stream-wise velocity. The decay of turbulence level is slower for the plane jet and hence the acoustic sources are present for longer distance along the downstream direction. Subsonic impinging jets are composed of four regions, the jet core, the fully developed jet, the impingement zone and the wall jet. The presence of the second region (fully developed free jet) depends on the distance of the wall from the nozzle and the length of the jet core. In impinging jets, reflection from the wall and the wall jet are additional sources of noise compared to the free jets. The results are analysed for the contribution of the different regions of the flow towards the radiated sound field. LES simulations of impinging round jets and impinging plane jet were carried out for this purpose. In addition, the results have been compared with equivalent free jets. The directivity plots showed that the SPL levels are significantly higher for the impinging jets at all angles. For free jets, a typical time scale for the acoustic sources is the ratio of the nozzle size to the jet velocity. This is ro/Uj for round jets and h/Uj for plane jets. For impinging jets, the non-dimensionlised rms of Lighthill’s source indicates that the time scale for acoustic sources is the ratio of the height of the nozzle from the wall to the jet velocity be L/Uj. LES of impinging round jets was carried out for two cases with different inflow perturbations. The jets were at Reynolds number of 88000 and Mach number of 0.9, same as the free jet cases. The impingement wall was at a distance L = 24ro from the nozzle exit. For impinging round jets, the SPL levels are found to be higher than the equivalent free jets. From the SPL levels and radiated noise spectra it was shown that the contribution from the large scale structures and its reflection from the wall is directional and at small angles to the wall normal. The difference in the range of angles where the radiation from the large scale structures were observed shows the significance of refraction of sound waves inside the flow. The rms values of the Lighthill’s sources indicate two dominant regions for the sources, just downstream of jet breakdown and in the impingement zone. The LES of impinging plane jet was done for a jet of Mach number 0.5 and Reynolds number of 6000. The impingement wall was at a distance L = 10h from the nozzle exit. The radiated sound field appears to emanate from this impingement zone. The directivity and the spectrum plots of the far field SPL indicate that there is no preferred direction of radiation from the impingement zone. The Lighthill’s sources are concentrated mainly in the impingement zone. The rms values of the sources indicate that the peak values occur in the impingement zone. The results from the different flow situations demonstrates the capability of LES with explicit filtering method in predicting the turbulent flow and radiated noise field. The method is robust and has been successfully used for moderate Reynolds number and an Euler simulation. An important feature is that LES can be used to identify acoustic sources and its convective speeds. It has been shown that the Lighthill source calculations, the calculated sound field and the observed radiation patterns agree well. An explanation for these based on the different turbulent flow structures has also been provided.

Acinetobacter baumannii is an increasingly multidrug-resistant pathogen contributing to hospital-acquired infections necessitating the discovery of novel treatments. A bacterial second messenger, cyclic diguanosine monophosphate (cyclic di-GMP), can regulate various persistence factors that are potentially advantageous for survival in hospital environments. Cyclic di-GMP–modulating enzymes and cyclic di-GMP–binding effectors predictively are encoded in the Acinetobacter baumannii genome. I hypothesized that cyclic di-GMP controls motility, biofilm formation, and desiccation tolerance in Acinetobacter baumannii. Disrupting cyclic di-GMP–modulating enzymes or cyclic di-GMP–binding effectors should alter the regulatory effectiveness of these phenotypes. I tested the multidrug-resistant isolate Acinetobacter baumannii strain AB5075 and identified several transposon mutants that altered twitching motility, biofilm formation, and desiccation tolerance; these results suggest that cyclic di-GMP plays a role during these three responses in Acinetobacter baumannii AB5075. Inhibiting these cyclic di-GMP signaling pathways could produce novel mechanisms to combat this pathogen in the hospital environment.

Acinetobacter baumannii is an increasingly multidrug-resistant pathogen contributing to hospital-acquired infections, necessitating a greater understanding of how it interacts with its surroundings. Many bacteria utilize different methods of bacterial motility to move about and interact with these surroundings. A bacterial second messenger, cyclic diguanosine monophosphate (c-di-GMP), can regulate various motility factors that are potentially advantageous for survival in and adaptation to their environment. Concentrations of c-di-GMP are regulated by specific synthesizing and degrading enzymes. Controlled levels of c-di-GMP allow interaction between the c-di-GMP and its binding effectors that induce changes in bacterial phenotypes such as biofilm formation and motility. A search of the A. baumannii genome identified two proteins that contain the c-di-GMP-binding PilZ domain. The PilZ protein for which this PilZ domain was named was initially discovered in Pseudomonas aeruginosa where it has been demonstrated to be a part of the type IV pilus machinery. Type IV pili play roles in twitching motility, adhering to surfaces, DNA uptake, protein secretion, and predation. One of the PilZ-containing proteins from A. baumannii resembled this original PilZ protein (PilZ), while the second PilZ-containing protein contained a hydrolase domain with unknown substrate specificity (HydP). I investigated whether these PilZ-containing proteins play a role in motility of A. baumannii by testing two strains: AB5075 that displays twitching motility, and ATCC17978 that displays an uncharacterized form of surface-associated motility. Results suggest PilZ plays a role in twitching motility, while its effect on surface-associated motility phenotypes3 is possibly due to polar effects from mutation. Results also suggest HydP plays a role in surface-associated motility, although its mechanism is not understood. Testing of both proteins’ PilZ domains indicates they may not bind c-di-GMP, implying they may be playing roles in motility regulation through other mechanisms outside of binding c-di-GMP. These findings give us greater insight into the regulatory mechanisms used by A. baumannii to move about its environment.