Type IV pili, or fimbriae, are long, thin proteinaceous appendages found on the surface of many well-known pathogens. They mediate a variety of important virulence functions for the organism, such as twitching motility, biofilm formation, uptake of genetic material and host cell recognition and adhesion. Pili are formed by the rapid polymerization and de-polymerization of the pilin subunit, and this is orchestrated by a complex macromolecular machine which spans the bacterial cell envelope, requiring a variety of gene products. The type IV pilus biogenesis system is closely related to the bacterial type II secretion system, one of six designated multi-protein cell envelope complexes which are dedicated to the specific secretion of exotoxins and virulence factors. Many of these secretion systems also produce fimbrial structures to facilitate the extrusion of their substrates or to communicate with the host. As they form crucial virulence factors, the secretion systems and the type IV pilus biogenesis system have become attractive potential antimicrobial targets and obtaining structural and functional information for the components of these systems is an important first step towards achieving this.Type IV pili appear on the surface of bacteria through an outer membrane pore, PilQ, which is a member of the secretin family. Secretins are also found in the type II and III secretion systems, but the way in which they are regulated remains unclear. PilQ forms a dodecameric chamber in the outer membrane with a large vestibule which reaches into the periplasm, composed of its N-terminal domains. In this project, N-terminal domains from PilQ were produced in recombinant form and their structures determined by NMR. One of these domains revealed an eight-stranded beta-sandwich structure which appears to be unique to type IV pilus secretins and has not been structurally characterized before. Another revealed an alpha/beta type fold which is common to secretins of other systems. In the second part of this project, the interaction formed between the N-terminal alpha/beta domains of PilQ and an essential inner membrane-anchored lipoprotein, PilP, was probed by NMR chemical shift perturbation. Based on changes to the 15N-HSQC spectra the binding site was mapped onto each protein to produce a computational model for the complex formed between the two. Using a recent cryo-EM structure for the Neisseria PilQ dodecamer determined by colleagues, it was possible to model the PilQ N-terminal domains in complex with PilP into the electron density map. This produced a model for the trans-periplasmic assembly formed by PilQ and PilP in the type IV pilus biogenesis system, and led to the conclusion that the PilQ dodecamer needs to disassemble considerably at the base to accommodate a pilus fibre. The novel beta-domains might therefore function to gate or open the secretin, and PilP may play a role in stabilizing the secretin during this and serve to connect the outer and inner membrane system components.

This thesis deals with the work Liber de coronatione Karoli IV. imperatoris (Book on the coronation of Emperor Charles IV) from the middle of the 14th century. Its author Iohannes Porta de Annoniaco was a personal secretary and confidant of Cardinal Peter of Colombier who was commissioned by Pope Innocent VI to perform the imperial coronation of Charles IV in Rome in 1355. As an eyewitness, Iohannes Porta describes the cardinal's and Charles's journey to Rome, focuses in more detail on the events in Rome, and above all, the very act of coronation. The author also deals with the following events of the return journey of both the cardinal and the emperor. In addition, he included in his work copies of documents and correspondence related to the coronation. The text offers a valuable source of direct testimony about the course of Charles's Italian journey. The thesis aims to present a Czech translation of selected parts of Iohannes Porta's text, supplemented by explanatory notes, the purpose of which is to clarify certain factual or linguistic particularities of the text. The translation is accompanied by an introductory study. Its first part explains the historical context of Charles's imperial coronation, the next part focuses on the author and the overall characteristics of the work.

The extracellular matrix (ECM), as the native cellular substrate, provides necessary mechanical and biological signals to cells. Cells exert forces in the nanonewton range, which when applied over time can strain extracellular matrix fibers until breakage. Cells and tissues inherently interact mechanically with their surrounding matrix, so tissue engineering materials would benefit from the ability to fully exploit mechanical-biochemical interactions to enhance integration with the human body. In this work, I developed an increased understanding of ECM fiber mechanical and mechano-biochemical properties. First, I generated novel composite ECM fibers that can be used to study combinations of ECM proteins in a controlled way. I determined how protein composition impacts mechanical properties of novel single ECM fibers in a hydrated state and showed how mechanical properties can be tuned through composition. Next, I assayed for strain and heparin-sensitive allosteric binding of ligands to fibronectin and fibrin fibers, and determined that the binding of two key growth factors is impacted by strain and heparin. Finally, I investigated the impact of fiber strain, heparin-pretreatment, and growth factor interactions on endothelial cell migration. The novel contributions of this project are the generation of new composite extracellular matrix fiber types with tunable mechanical properties, as well as the identification of extracellular matrix protein mechanosensitive and heparin-sensitive interactions with growth factors and their impact on endothelial cell migration, which could be used to aid in the design of protein-based biomaterials for cardiovascular applications. / 2024-05-23T00:00:00Z

Introduction. N-acetylcysteine (NAC) is the antidote for acetaminophen (Tylenol) toxicity from over ingestion leading to 56,000 emergency room visits yearly. This is worrisome due to the risk of hepatoxicity, especially in children and adolescents. Often, nausea and vomiting are associated with NAC use and is treated acutely by ondansetron (Zofran), a 5-HT3 receptor antagonist. Inconveniently, the NAC 21-hour intravenous (IV) infusion needs to be halted with IV flushing before ondansetron can be administered. Another IV flushing follows before NAC is resumed. This causes treatment interruption in a medical emergency; therefore, we are investigating the IV compatibility of NAC and ondansetron to reduce the steps in treating acute nausea/vomiting. Methods. A reverse phase high-performance liquid chromatography (RP-HPLC) method was utilized for NAC quantification. The analysis was conducted on an Agilent Eclpise XDB-C18 column (3.5 micron, 4.6 x 150 mm) with a mobile phase containing acetonitrile (ACN), water (10:90 v/v), and 0.1 % trifluoroacetic acid (TFA). The flow rate was set at 0.500 mL/min with an injection volume of 10 microliters and a temperature of 50oC. A UV wavelength of 212 nm was utilized for detection of NAC. A liquid chromatography mass spectrometry (LC – MS/MS) method was able to quantify levels of ondansetron. A Waters XBridge C18 column (3.5 micron, 4.6 x 150 mm) was used for separation of ondansetron. The mobile phase included ammonium formate buffer (pH 3.0, 5 mM) and acetonitrile (15:85, v/v) with the flow rate set at 0.500 mL/min. Electrospray ionization interface is set in the positive mode for measurement of ondansetron using a precursor ion of m/z 294.0200. Results. The HPLC-UV and LC-MS/MS methods for NAC and ondansetron, respectively, will be validated for linearity, precision and accuracy. Then the methods will be applied toward a chemical compatibility investigation of NAC and ondansetron through medical grade tubing and y-site. The ideal outcome would be to confidently assume NAC and ondansetron are IV compatible for y-site administration to avoid infusion interruption for treatment of acetaminophen toxicity. Conclusion. IV compatibility for NAC and ondansetron affords no infusion interruptions reducing unnecessary risk of acetaminophen toxicity. This also decreases risk of medical errors based on the multi-step process to administer ondansetron with receiving NAC. Overall, compatibility could create safer, more efficient protocols for treatment of acute nausea/vomiting from NAC administration.

Geobacter sulfurreducens possesses type IV pili that are considered to be conductive nanowires and a crucial structural element in biofilm formation, enabling electron transfer to insoluble metal oxides in anaerobic sediments and to graphite anodes in microbial fuel cells. The molecular mechanism by which electrons are transferred through the nanowires to the electron acceptor is not fully understood. Prior to the work described in this thesis, the gene (pilA) encoding the structural pilus subunit had been identified, but little was known about the functional translation start codon, the length of the mature secreted protein, or what renders the pili conductive. Using mass spectrometry, I found that a tyrosine residue (Y32) near the carboxyl terminus of the mature PilA protein is posttranslationally modified by attachment of glycerophosphate. I studied the significance of Y32 for biofilm formation on various surfaces and for growth of G. sulfurreducens with insoluble electron acceptors. A mutant in which Y32 was replaced by phenylalanine lacked the glycerophosphate; biofilm formation on graphite surfaces was severely diminished and current production in microbial fuel cells was initiated only after a long lag phase. Moreover, cells with Y32F mutation in the pilA gene exhibited growth deficiency when Fe(III) oxide was the sole electron acceptor. My data confirm the role of G. sulfurreducens pili in biofilm formation and electron transfer to Fe(III) oxide and identify an amino acid in the PilA protein that is essential for these two processes. I also confirmed the existence of two functional translation start codons for the pilA gene and identified two isoforms (short and long) of the PilA preprotein by series of genetic complementation experiments. The short PilA isoform is found predominantly in an intracellular fraction, and seems to stabilize the long isoform and influence the secretion of several outer surface c-type cytochromes. The long PilA isoform, on the other hand, is required for secretion of PilA to the outer surface of the cell, a process that requires co-expression of pilA and the nine genes on its 3’ side. The long isoform is essential for biofilm formation on various surfaces, for optimum current production in microbial fuel cells, and for growth on insoluble Fe(III) oxide. This study provides new insight concerning the function and biogenesis of Geobacter type IV PilA, as well as a foundation for further research that will be conducted on microbial nanowires.

Type IV pili (T4P) are long, thin, flexible surface appendages used by various bacteria for surface adhesion, cell-cell aggregation, DNA uptake, biofilm formation and motility. Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, and uses T4P as a key virulence factor to infect immunocompromised individuals. Four subcomplexes make up a functional T4P system in P. aeruginosa and the role of the alignment subcomplex is to physically connect the outer membrane pore with the inner membrane motor, allowing for efficient extrusion of the pilus fibre from the cell. Two alignment subcomplex proteins, PilN and PilO, form heterodimers and are required for proper function of the system. These proteins may be able to transduce signals between various T4P components to indicate extension and/or retraction of the pilus fibre. This thesis focused on characterization of the interaction interfaces between PilN and PilO, and on understanding the dynamics required for proper function of the system. We show that although PilN and PilO make extensive interaction contacts throughout their lengths, single point substitutions at key residues can successfully disrupt the function of the T4P system. Crosslinking PilN and PilO as homo- or heterodimers can disrupt motility and surface piliation, indicating that interfaces between these proteins must be dynamic to allow proper T4P function. A high resolution X-ray crystal structure of PilO was solved and exhibits new structural features previously unidentified. This work furthers our understanding of the structures and regions of interaction between PilN and PilO, as well as defining a role for these proteins in extension and retraction. / Dissertation / Doctor of Philosophy (PhD) / Pseudomonas aeruginosa is an opportunistic bacterium, able to infect individuals with weakened immune systems. It attaches to and moves along surfaces using long, thin, sticky, retractable fibres known as type IV pili. Similar to a grappling gun, a functional type IV pilus system requires four subcomplexes working in unison to allow for the extension, adherence, and retraction of pilus fibres, which pulls the cell forward towards the point of attachment. Two key proteins, PilN and PilO, are bound to each other and allow for efficient extension and retraction of the pilus fibre. This study focused on characterization of the interactions of PilN and PilO, and on understanding whether dynamic rearrangements of the interfaces between these proteins is required for proper function of the system. We show that although these proteins have extensive interaction interfaces, single residue substitutions in either of them can disrupt the ability of the bacteria to properly extend and/or retract their pili. This work furthers our understanding of the structures and regions of interaction between PilN and PilO, providing information that might allow disruption of these interfaces to block bacterial attachment or motility, both of which are important for infection.

Type IVa pili (T4aP) are long, retractile, filamentous, surface appendages involved in cellular surface adhesion, biofilm formation, DNA uptake, and a unique form of motility called ‘twitching’. They are a critical virulence factor in a number of bacteria, including the opportunistic pathogen Pseudomonas aeruginosa, a major cause of hospital-acquired infections. T4aP function is controlled by a number of different regulatory proteins and systems. A putative chemosensory system termed ‘Chp’, controls levels of the second messenger molecule cyclic adenosine monophosphate (cAMP). cAMP works with a cAMP receptor protein called Vfr to control expression of ~200 virulence genes, including those that are required to make T4aP. cAMP levels are regulated by proteins outside the Chp system, including the bitopic inner membrane protein, FimV. This study examines the role of the Chp system and FimV in T4aP regulation. Both proteins are required for regulation of cAMP levels, while the Chp system also has a cAMP-independent role in regulating twitching. FimV has been shown to regulate cAMP levels, possibly connecting to the Chp system through a scaffold protein, FimL. We present the structure of a conserved cytoplasmic region of FimV, and show that this region is required for connecting FimV to the Chp system. We also characterize the cAMP-independent role of FimV, confirming that it is distinct from that of the Chp system, and is involved in localizing T4P regulatory proteins. We also provide evidence that the cAMP-independent role of the Chp system is to mediate the balance between T4P extension and retraction, possibly through denoting the ‘front’ of a motile cell. Together, these data help to resolve the cAMP-independent and –dependent pathways controlling twitching motility. / Thesis / Doctor of Philosophy (PhD) / Pseudomonas aeruginosa is a bacterium that causes infection in people with weakened immune systems. One key factor it uses to cause infection is the type IVa pilus (T4aP), a filamentous appendage displayed on the cell surface. T4aP can repeatedly extend and retract, and are involved in attachment to host cells, and movement along surfaces. When T4aP cannot extend or retract, the bacteria cannot cause infection. Many proteins work together to control T4aP function – this study focuses on two of them. They have one overlapping function, controlling levels of a signalling molecule needed to make T4aP. We also show that they have a second, non-overlapping function. One is involved in controlling the extension/retraction balance, possibly by marking the front of a cell, while the other may localize pilus-related proteins within a cell. This work helps us understand how P. aeruginosa makes T4aP, and provides information helpful to understanding control of virulence.

Pseudomonas aeruginosa uses type IV pili (T4P) to colonize various materials and for surface-associated twitching motility. We previously identified five phylogenetically-distinct alleles of pi/A in P. aeruginosa, four of which occur in genetic cassettes with specific accessory genes (Kus et al., Microbiology 150:1315-1326, 2004). Each of the five pilin alleles, with and without its associated pilin accessory gene, was used to complement a group II PA01 pi/A mutant. Expression of group I or IV pi/A genes restored twitching motility to the same extent as the PA01 group II pilin. In contrast, complementation with group Ill or group V pi/A genes resulted in poor twitching that increased significantly when the cognate tfp Y or tfpZ accessory genes were cointroduced. The enhanced motility was linked to an increase in recoverable surface pili, and not to alterations in total pilin pools. Expression of the pilin genes, with or without accessory genes, in a PA01 pi/A-pi/T double mutant background resulted in expression of large amounts of surface pili, suggesting that the accessory proteins function to modulate pilin retraction dynamics. Reduction of twitching motility and surface piliation was also observed a tfpYknockout mutant of group Ill strain PA14, confirming that the accessory proteins enhance pilus assembly on the cell surface. The accessory proteins are specific for their cognate pilins; a PilAv-TfpY chimera produced few surface pili, resembling the phenotype of PA01 complemented with pi!Av alone. The linkage between specific pilin and accessory genes may be evolutionarily conserved because the accessory proteins antagonize pilus retraction, increasing pilus expression on the cell surface and thereby enhancing function. / Thesis / Master of Science (MSc)

Le mélanome est le cancer cutané le plus invasif. Au cours de l’invasion tumorale et de la dissémination métastatique, les cellules tumorales sont capables de dégrader la matrice extracellulaire par la sécrétion de protéases telles que les MMPs. Lors de cette protéolyse matricielle, différents fragments de la matrice extracellulaire exerçant des activités anti-tumorale et/ou anti-angiogénique, nommés matrikines, sont libérés et modulent la croissance tumorale. De nombreuses matrikines dérivées des collagènes de membrane basale sont capables de limiter la progression tumorale. Nous avons étudié les propriétés anti-tumorales du domaine NC1 α4(IV), nommé tétrastatine, à la fois in vitro et in vivo dans un modèle de mélanome humain. La tétrastatine induit une inhibition de la prolifération et de l’invasion des cellules de mélanome in vitro. L’inhibition de prolifération est corrélée à un retard en phase G1/S du cycle cellulaire en présence de tétrastatine. L’inhibtion de l’invasion peut notamment s’expliquer par une inhibition de l’activation de la MMP-14 et une modification de sa répartition cellulaire, avec perte du phénotype migratoire en présence de tétrastatine. In vivo, la surexpression de la tétrastatine induit une forte inhibition de la croissance tumorale, dans un modèle de xénogreffe de mélanome humain chez la souris nude. Nous avons également pu identifier l’intégrine αvβ3 comme un récepteur potentiel de la tétrastatine. Enfin, l’étude des capacités anti-prolifératives et anti-invasives des cellules UACC 903 en présence de différents peptides permet aujourd’hui de mieux préciser la séquence responsable de l’activité anti-tumorale de ce domaine. En conclusion, la tétrastatine est une nouvelle matrikine à fort potentiel anti-tumoral capable de limiter la progression du mélanome. / Melanoma is the most invasive cutaneous cancer. During tumor invasion and metastatic dissemination, tumor cells degrade the extracellular matrix by secretion of proteases such as MMPs. During matrix proteolysis, fragments of the extracellular matrix with anti-tumor and/or anti-angiogenic activities, called matrikines, are released and modulate tumor growth. Many matrikines derived from basement membrane collagens are able to inhibit tumor progression. We studied the anti-tumor properties of the domain NC1 α4 (IV), named tetrastatin, both in vitro and in vivo in a human melanoma model. Tetrastatin induces inhibition of proliferation and invasion of melanoma cells in vitro. This inhibition of proliferation is correlated to a cell cycle delay in G1/S phase when cells are incubated with tetrastatin. The inhibition of invasion could be due, at least partly, to the inhibition of MMP-14 active form and modification of its cellular distribution, with a loss of the migratory phenotype in the presence of tetrastatin. In vivo, tetrastatin overexpression induces a strong inhibition of tumor growth, in a human melanoma xenograft model in nude mice. We also identified integrin αvβ3 as a potential receptor of tetrastatin. Finally, the study of the anti-proliferative and anti-invasive properties of the UACC 903 cells in the presence of different peptides allows us to better identify the sequence responsible of the anti-tumor activity. In conclusion, tetrastatin is a new potent anti-tumor matrikine capable of limiting melanoma progression.

Dipeptidyl peptidase IV (DPP-IV) is a serine protease, which executes its proteolytic activity by cleaving X-Pro dipeptides from the N-termini of its substrates. Furthermore, DPP-IV exhibits many biological functions independent of its enzymatic aktivity. Previous studies in our laboratory proved increased expression of DPP-IV in high-grade astrocytic tumours. To evaluate the enzymatic and non-enzymatic functions of DPP-IV in a glioma model, clones of asctrocytic cell line U373MG transfected by enzymatically inactive, mutated DPP-IV (mutDPP-IV) and enzymatically active, wild type DPP-IV (wtDPP-IV), were prepared. Enzymatically inactive mutDPP-IV was prepared using point mutation the active site serine residue. Cells U373MG were transfected using a doxycycline inducible Tet-On® system. For further analysis of the transgenic forms of DPP-IV, methods were used for verification of protein expression, enzymatic activity and subcellular localization. Doxycycline induced U373MG mutDPP-IV and U373MG wtDPP-IV cells, expressing mutated and wild type DPP-IV, respectivelly, exhibited increased expression of transgenic DPP-IV in a concentration and time dependent manner. Doxycycline induced U373MG wtDPP-IV cells exhibited both increased expression and enzymatic activity of DPP-IV. In contrast, DPP-IV enzymatic...