Understanding the zooplankton ammonium excretion: from biogeochemical implications to intracellular regulatory mechanisms

[EN] This thesis focuses on the zooplankton NH4+ regeneration that supports about the 80% of the phytoplankton requirements. In its more oceanographic facet, it elucidates the control that the mesozooplankton community exerts on the primary productivity in the northern Benguela, and models the N-fluxes from zooplankton NH4+ excretion. At the physiological level, it examines the relationship between the NH4+ excretion and its associated biochemistry. Assuming the substrate availability as the critical factor in regulating the velocity of NH4+ production, a bisubstrate model was developed to predict its actual rate in zooplankton. Overall, this research provides knowledge about the implications of zooplankton NH4+ excretion on the biogeochemical cycles, and introduces new insights into the study of this process from enzymatic measurements.

Understanding the zooplankton ammonium excretion : from biogeochemical implications to intracellular regulatory mechanisms

[EN]Zooplankton play a key role in marine ecosystems and their biogeochemical cycles. They exert control over the primary productivity through the consumption of organic matter and, at the same time, the release of nutrients that sustains the phytoplankton growth. This thesis focuses on the NH+ 4 excretion processes related to these heterotrophic organisms that support, at a global scale, about the 80% of the phytoplankton requirements. However, thereisno clear constant pattern in the zooplankton contribution to theNH+ 4 regeneration throughout thedifferent pelagic ecosystems, so continuousmonitoring of thismetabolic processisessential at widetemporal and spatial scales...

Risposte di resistenza a batteri fitopatogeni di importanti specie coltivate indotte da molecole segnale di diversa natura

A modern management of crop protection should be based on integrated control programmes, including the use of environmentally safe products. Antagonistic/beneficial bacteria and resistance inducers may have a great potential in the prophylaxis of diseases caused by common and quarantine pathogens. This work was carried out to confirm the ability of the known strain IPV-BO G19 (Pseudomonas fluorescens) against fire blight (Erwinia amylovora), as well as to evaluate their efficacy against southern bacterial wilt of tomato (Ralstonia solanacearum) and grapevine crown gall (Agrobacterium vitis). A virulent strain of R. solanacearum race 3 was inhibited by the antagonist on plate. When the pathogen was inoculated 48 h after their application to the root apparatus of tomato plants grown in a climatic chamber, bacterial wilt progression rate was clearly reduced. Moreover the defence response evoked by IPV-BO G19 was studied in tomato plants by monitoring the transcription of genes codifying for three PRs as PR-1a, PR-4, PR-5 and for an intracellular chitinase using multiplex RT-PCR and Real Time RT-PCR. In two field trials during 2005 and 2006, the strain IPV-BO G19 was compared with biofungicides and some abiotic elicitors to protect actively growing shoots of pear scions against fire blight. In both trials, IPV-BO G19 plus Na-alginate gave a high level of protection, three weeks after wound inoculation with E. amylovora. In pear leaf tissues treated with the antagonistic strain IPV-BO G19, catalase, superoxyde dismutase and peroxidise activity was evaluated as markers of induced resistance. The IPV-BO G19 strain was compared with other bioagents and resistance inducers to prevent grapevine crown gall under glasshouse and vineyard conditions.

Induktion und Signaltransduktion bei der Expression des Chemokins MCP-1 in Monozyten

Das Chemokin 'Monocyte Chemoattractant Protein-1' (MCP-1) spielt bei inflammatorischen Erkrankungen eine wesentliche Rolle. Verschiedene Zelltypen produzieren MCP-1. Es interessierte, welche Stimuli in Monozyten MCP-1 induzieren können und welche Signaltransduktionskaskaden daran beteiligt sind. Darüber hinaus sollte die Rolle einzelner Transkriptionsfaktoren und Promotorregionen des MCP-1-Gens untersucht werden.Komponenten Gram-positiver und -negativer Bakterien, Phorbolester und Substanzen, die die intrazelluläre Calciumkonzentration erhöhen, induzierten die MCP-1-Expression in einer humanen myelomonozytären Zellinie (THP-1) und in frisch isolierten Monozyten. Die mit Lipopolysaccharid (LPS)-induzierte MCP-1-Expression war stark von der MAPK/ERK-Kinase (MEK)-1/-2 und von I-kappaB Kinasen beziehungsweise NF-kappaB abhängig, dagegen scheinen Calcineurin, Calmodulinkinasen und die 'Mitogen-Activated Protein Kinase' p38 keine entscheidende Rolle zu spielen. Die Thapsigargin (TG)-induzierte MCP-1-Bildung durch Erhöhung der intrazellulären Calciumkonzentration war zusätzlich von Calcineurin und Calmodulinkinasen abhängig. Als nukleäre Transkriptionsfaktoren wurden bei der LPS-Stimulation NF-kappaB sowie AP-1 und zusätzlich NF-ATc3 bei Stimulation durch TG nachgewiesen. Die Untersuchung des MCP-1-Promotors konnte eine Bindung von NF-kappaB- und AP-1-Mitglieder an eine bislang nicht untersuchte distale Region und eine AP-1-Bindung an eine proximale Region nachweisen. Die Ergebnisse lassen den Schluß zu, daß die Aktivierung der MCP-1-Expression durch verschiedene Stimuli unter Beteiligung teilweise unterschiedlicher Signaltransduktionswege abläuft und sowohl eine proximale als auch eine distale Promotorregion des MCP-1-Gens daran beteiligt ist.

Use of sub-lethal high pressure homogenization (HPH) treatments to enhance functional properties of lactic acid bacteria probiotic strains

The aim of this PhD thesis was to evaluate the effect of a sub-lethal HPH treatment on some probiotic properties and on cell response mechanisms of already-known functional strains, isolated from Argentinean dairy products. The results achieved showed that HPH treatments, performed at a sub-lethal level of 50 MPa, increased some important functional and technological characteristics of the considered non intestinal probiotic strains. In particular, HPH could modify cell hydrophobicity, autoaggregation and resistance to acid gastric conditions (tested in in vitro model), cell viability and cell production of positive aroma compounds, during a refrigerate storage in a simulated dairy product. In addition, HPH process was able to increase also some probiotic properties exerted in vivo and tested for two of the considered strains. In fact, HPH-treated cells were able to enhance the number of IgA+ cells more than other not treated cells, although this capacity was time dependent. On the other hand, HPH treatment was able to modify some important characteristics that are linked to the cell wall and, consequently, could alter the adhesion capacity in vivo and the interaction with the intestinal cells. These modifications, involving cell outermost structures, were highlighted also by Trasmission Electron Microscopy (TEM) analysis. In fact, the micrographs obtained showed a significant effect of the pressure treatment on the cell morphology and particularly on the cell wall. Moreover, the results achieved showed that composition of plasma membranes and their level of unsaturation are involved in response mechanisms adopted by cells exposed to the sub-lethal HPH treatment. Although the response to the treatment varied according to the characteristics of individual strains, time of storage and suspension media employed, the results of present study, could be exploited to enhance the quality of functional products and to improve their organoleptic properties.

The role of the NG2 proteoglycan in migration and characterization of the interaction with the intracellular binding partner, Syntenin

NG2 is a transmembrane proteoglycan with two N-terminal LNS domains and a C-terminal PDZ-binding motif. It is expressed in the developing and adult CNS by oligodendroglial precursor cells and subpopulations of perisynaptic glia and elsewhere by many immature cell types. In order to elucidate the functions of the protein and the heterogenous cell population which expresses it, we undertook to identify and characterise interaction partners of the molecule. The presence of the C-terminal PDZ recognition site in NG2 suggested PDZ-domain proteins as intracellular binding partners. In this work, interaction between the PDZ protein Syntenin and NG2 has been characterised. Syntenin is known to be involved in plasma membrane dynamics, metastasis and adhesion. Syntenin may thus link NG2 to the cytoskeleton, mediating migration of developing oligodendrocytes to axonal tracts prior to myelination, as well as process movement of NG2+ perisynaptic glia. NG2 is involved in cell spreading and polyclonal antibodies against NG2 inhibit the migration of immature glia and cell lines expressing the molecule. In this work we have characterised the segments of the extracellular portion of NG2 that are involved in migration. We found that the extracellular region immediately preceding the transmembrane segment is most important for cell motility. As part of this thesis, biochemical approaches to identify a trans-binding ligand interacting with the extracellular part of NG2 was also explored.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Insights in the maturation of pathogenic bacteria vaccine candidates using mass spectrometry based approaches

The study of the maturation process that occurs to a protein is of pivotal importance for the understanding of its function. This is true also in the vaccine field but in this case is also important to evaluate if inappropriate protein conformation and maturation play roles in the impairment of the functional immunogenicity of protein vaccines. Mass spectrometry (MS) is the method of choice for the study of the maturation process since each modification that occurs during the maturation will lead to a change in the mass of the entire protein. Therefore the aim of my thesis is the development of mass spectrometry-based approaches to study the maturation of proteins and the application of these methods to proteic vaccine candidates. The thesis is divided in two main parts. In the first part, I focused my attention on the study of the maturation of different vaccine candidates using native mass spectrometry. The analyses in this case have been performed using recombinant proteins produced in E. coli. In the second part I applied different MS strategies for the identification of unknown PTMs on pathogenic bacteria surface proteins since modified surface proteins are now considered for vaccine candidate selection.

Biohydrogen production from food industry waste by suspended and immobilized thermophylic bacteria

This work describes hydrogen production by anaerobic digestion of glucose, molasses and milk whey by 4 thermophilic Thermotoga strains. In the attached-cell tests, the biofilm support characterized by the highest specific surface resulted in the best H2 rate. All the Thermotoga strains examined (T. neapolitana, T. maritima, T. naphtophila, T. petrophila) could produce H2 from glucose, molasses and milk whey, both in suspended- and attached-cell tests. With all the three substrates, the best performances were obtained with T. neapolitana. Some tests were conducted out to select the optimal carrier for the attached-cell conditions. 4 types of carrier were tested: 3 sintered glass carriers and a ceramic one; the chosen carrier was Biomax.

The silent survival of Staphylococcus aureus phagocyted by HL-60 derived neutrophils

Staphylococcus aureus is a Gram positive pathogen that causes various human infections and represents one of the most common causes of bacteremia. S. aureus is able to invade a variety of non-professional phagocytes and that can survive engulfment by neutrophils, producing both secreted and surface components that compromise innate immune responses. In the contest of our study we evaluated the functional activity of vaccine specific antibodies by opsonophagocytosis killing assay (OPKA). Interestingly a low level of killing of the staphylococcal cells has been observed. In the meanwhile intracellular survival studies showed that S. aureus persisted inside phagocytes for several hours until a burst of growth after 5 hours in the supernatant. These data suggest that the strong ability of S. aureus to survive in the phagocytes could be the cause of the low killing measured by OPKA. Moreover parallel studies on HL-60 cells infected with S. aureus done by using transmission electron microscopy (TEM) interestingly showed that staphylococcal cells have an intracellular localization (endosomal vacuoles) and that they are able not only to maintain the integrity of their membrane but also to replicate inside vacuolar compartments. Finally in order to generate 3D volume of whole bacteria when present inside neutrophilic vacuoles, we collected a series of tomographic two-dimensional (2D) images by using a transmission electron microscope, generating 5 different tomograms. The three-dimensional reconstruction reveals the presence of intact bacteria within neutrophil vacuoles. The S. aureus membrane appears completely undamaged and integral in contrast with the physiological process of phagosytosis through vacuoles progression. S. aureus bacteria show a homogenous distribution of the density in all the three dimensions (X, Y, Z). All these evidences definitely explain the ability of the pathogen to survive inside the endosomal vacuoles and should be the cause of the low killing level.