Weakening of the Gram-negative bacterial outer membrane - A tool for increasing microbiological safety

Gram-negative bacteria are harmful in various surroundings. In the food industy their metabolites are potential cause of spoilage and this group also includes many severe or potential pathogens, such as Salmonella. Due to their ability to produce biofilms Gram-negative bacteria also cause problems in many industrial processes as well as in clinical surroundings. Control of Gram-negative bacteria is hampered by the outer membrane (OM) in the outermost layer of the cells. This layer is an intrinsic barrier for many hydrophobic agents and macromolecules. Permeabilizers are compounds that weaken OM and can thus increase the activity of antimicrobials by facililating entry of hydrophobic compounds and macromolecules into the cell where they can reach their target sites and inhibit or destroy cellular functions. The work described in this thesis shows that lactic acid acts as a permeabilizer and destabilizes the OM of Gram-negative bacteria. In addition, organic acids present in berriers, i.e. malic, sorbic and benzoic acid, were shown to weaken the OM of Gram-negative bacteria. Organic acids can poteniate the antimicrobial activity of other compounds. Microbial colonic degradation products of plant-derived phenolic compounds (3,4-dihydroxyphenylacetic acid, 3-hydroxyphenylacetic acid, 3,4-dihydroxyphenylpropionic acid, 4-hydroxyphenylpropionic acid, 3-phenylpropionic acid and 3-hydroxyphenylpropionic acid) efficiently destabilized OM of Salmonella. The studies increase our understanding of the mechanism of action of the classical chelator, ethylenediaminetetra-acetic acid (EDTA). In addition, the results indicate that the biocidic activity of benzalkonium chloride against Pseudomonas can be increased by combined use with polyethylenimine (PEI). In addition to PEI, several other potential permeabilizers, such as succimer, were shown to destabilize the OM of Gram-negative bacteria. Furthermore, combination of the results obtained from various permeability assays (e.g. uptake of a hydrophobic probe, sensitization to hydrophobic antibiotics and detergents, release of lipopolysaccharide (LPS) and LPS-specific fatty acids) with atomic force microscopy (AFM) image results increases our knowledge of the action of permeabilizers.

Coherent potential approximation, averaged T-matrix approximation and Lloyd's model

It is shown how the single-site coherent potential approximation and the averaged T-matrix approximation become exact in the calculation of the averaged single-particle Green function of the electron in the Anderson model when the site energy is distributed randomly with lorentzian distribution. Using these approximations, Lloyd's exact result is reproduced.

Study of linear and nonlinear optical properties of dendrimers using density matrix renormalization group method

We have used the density matrix renormalization group (DMRG) method to study the linear and nonlinear optical responses of first generation nitrogen based dendrimers with donor acceptor groups. We have employed Pariser–Parr–Pople Hamiltonian to model the interacting pi electrons in these systems. Within the DMRG method we have used an innovative scheme to target excited states with large transition dipole to the ground state. This method reproduces exact optical gaps and polarization in systems where exact diagonalization of the Hamiltonian is possible. We have used a correction vector method which tacitly takes into account the contribution of all excited states, to obtain the ground state polarizibility, first hyperpolarizibility, and two photon absorption cross sections. We find that the lowest optical excitations as well as the lowest excited triplet states are localized. It is interesting to note that the first hyperpolarizibility saturates more rapidly with system size compared to linear polarizibility unlike that of linear polyenes.

Matrix Decomposition Methods for Data Mining : Computational Complexity and Algorithms

Matrix decompositions, where a given matrix is represented as a product of two other matrices, are regularly used in data mining. Most matrix decompositions have their roots in linear algebra, but the needs of data mining are not always those of linear algebra. In data mining one needs to have results that are interpretable -- and what is considered interpretable in data mining can be very different to what is considered interpretable in linear algebra. --- The purpose of this thesis is to study matrix decompositions that directly address the issue of interpretability. An example is a decomposition of binary matrices where the factor matrices are assumed to be binary and the matrix multiplication is Boolean. The restriction to binary factor matrices increases interpretability -- factor matrices are of the same type as the original matrix -- and allows the use of Boolean matrix multiplication, which is often more intuitive than normal matrix multiplication with binary matrices. Also several other decomposition methods are described, and the computational complexity of computing them is studied together with the hardness of approximating the related optimization problems. Based on these studies, algorithms for constructing the decompositions are proposed. Constructing the decompositions turns out to be computationally hard, and the proposed algorithms are mostly based on various heuristics. Nevertheless, the algorithms are shown to be capable of finding good results in empirical experiments conducted with both synthetic and real-world data.

Role of Capping Ligands on the Nanoparticles in the Modulation of Properties of a Hybrid Matrix of Nanoparticles in a 2D Film and in a Supramolecular Organogel

We incorporate various gold nanoparticles (AuNPs) capped with different ligands in two-dimensional films and three-dimensional aggregates derived from N-stearoyl-L-alanine and N-lauroyl-L-alanine, respectively. The assemblies of N-stearoyl-L-alanine afforded stable films at the air-water interface. More compact assemblies were formed upon incorporation of AuNPs in the air-water interface of N-stearoyl-L-alanine. We then examined the effects of incorporation of various AuNPs functionalized with different capping ligands in three-dimensional assemblies of N-lauroyl-L-alanine, a compound that formed a gel in hydrocarbons. The profound influence of nanoparticle incorporation into physical gels was evident from evaluation of various microscopic and bulk properties. The interaction of AuNPs with the gelator assembly was found to depend critically on the capping ligands protecting the Au surface of the gold nanoparticles. Transmission electron microscopy (TEM) showed a long-range directional assembly of certain AuNPs along the gel fibers. Scanning electron microscopy (SEM) images of the freeze-dried gels and nanocomposites indicate that the morphological transformation in the composite microstructures depends significantly on the capping agent of the nanoparticles. Differential scanning calorimetry (DSC) showed that gel formation from sol occurred at a lower temperature upon incorporation of AuNPs having capping ligands that were able to align and noncovalently interact with the gel fibers. Rheological studies indicate that the gel-nanoparticle composites exhibit significantly greater viscoelasticity compared to the native gel alone when the capping ligands are able to interact through interdigitation into the gelator assembly. Thus, it was possible to define a clear relationship between the materials and the molecular-level properties by means of manipulation of the information inscribed on the NP surface.

Applicability of pebble matrix filtration for the pre-treatment of surface waters containing high turbidity and NOM

Purification of drinking water is routinely achieved by use of conventional coagulants and disinfection procedures. However, there are instances such as flood events when the level of turbidity reaches extreme levels while NOM may be an issue throughout the year. Consequently, there is a need to develop technologies which can effectively treat water of high turbidity during flood events and natural organic matter (NOM) content year round. It was our hypothesis that pebble matrix filtration potentially offered a relatively cheap, simple and reliable means to clarify such challenging water samples. Therefore, a laboratory scale pebble matrix filter (PMF) column was used to evaluate the turbidity and natural organic matter (NOM) pre-treatment performance in relation to 2013 Brisbane River flood water. Since the high turbidity was only a seasonal and short term problem, the general applicability of pebble matrix filters for NOM removal was also investigated. A 1.0 m deep bed of pebbles (the matrix) partly in-filled with either sand or crushed glass was tested, upon which was situated a layer of granular activated carbon (GAC). Turbidity was measured as a surrogate for suspended solids (SS), whereas, total organic carbon (TOC) and UV Absorbance at 254 nm were measured as surrogate parameters for NOM. Experiments using natural flood water showed that without the addition of any chemical coagulants, PMF columns achieved at least 50% turbidity reduction when the source water contained moderate hardness levels. For harder water samples, above 85% turbidity reduction was obtained. The ability to remove 50% turbidity without chemical coagulants may represent significant cost savings to water treatment plants and added environmental benefits accrue due to less sludge formation. A TOC reduction of 35-47% and UV-254 nm reduction of 24-38% was also observed. In addition to turbidity removal during flood periods, the ability to remove NOM using the pebble matrix filter throughout the year may have the benefit of reducing disinfection by-products (DBP) formation potential and coagulant demand at water treatment plants. Final head losses were remarkably low, reaching only 11 cm at a filtration velocity of 0.70 m/h.

Mechanical properties of nanodiamond-reinforced polymer-matrix composites

Poly(vinyl alcohol)-matrix reinforced with nanodiamond (ND) particles, with ND content up to 0.6 wt%, were synthesized. Characterization of the composites by transmission electron microscopy (TEM) and small angle X-ray scattering (SAXS) reveal uniform distribution of the ND particles with no agglomeration in the matrix. Differential scanning calorimetry reveals that the crystallinity of the polymer increases with increasing ND content, indicating a strong interaction between ND and PVA. Nano-indentation technique was employed to assess the mechanical properties of composites. Results show that even small additions of ND lead to significant enhancement in the hardness and elastic modulus of PVA. Possible micromechanisms responsible for the enhancement of the mechanical properties are discussed.

Velocity ratio-cum-transfer matrix method for the evaluation of a muffler with mean flow

The paper deals with a method for the evaluation of exhaust muffers with mean flow. A new set of variables, convective pressure and convective mass velocity, have been defined to replace the acoustic variables. An expression for attenuation (insertion loss) of a muffler has been proposed in terms of convective terminal impedances and a velocity ratio, on the lines of the one existing for acoustic filters. In order to evaluate the velocity ratio in terms of convective variables, transfer matrices for various muffler elements have been derived from the basic relations of energy, mass and momentum. Finally, the velocity ratiocum-transfer matrix method is illustrated for a typical straight-through muffler.

On the transfer matrix for a uniform tube with a moving medium

Abstract is not available.

Optimal iterative schemes for computing the Moore-Penrose matrix inverse

Among the iterative schemes for computing the Moore — Penrose inverse of a woll-conditioned matrix, only those which have an order of convergence three or two are computationally efficient. A Fortran programme for these schemes is provided.

Rank-Augmented LU-Algorithm for Computing Generalized Matrix Inverses

A rank-augmnented LU-algorithm is suggested for computing a generalized inverse of a matrix. Initially suitable diagonal corrections are introduced in (the symmetrized form of) the given matrix to facilitate decomposition; a backward-correction scheme then yields a desired generalized inverse.

Structural and Functional Studies on Trimeric Autotransporters

Trimeric autotransporters are a family of secreted outer membrane proteins in Gram-negative bacteria. These obligate homotrimeric proteins share a conserved C-terminal region, termed the translocation unit. This domain consists of an integral membrane β-barrel anchor and associated α-helices which pass through the pore of the barrel. The α-helices link to the extracellular portion of the protein, the passenger domain. Autotransportation refers to the way in which the passenger domain is secreted into the extracellular space. It appears that the translocation unit mediates the transport of the passenger domain across the outer membrane, and no external factors, such as ATP, ion gradients nor other proteins, are required. The passenger domain of autotransporters contains the specific activities of each protein. These are usually related to virulence. In trimeric autotransporters, the main function of the proteins is to act as adhesins. One such protein is the Yersinia adhesin YadA, found in enteropathogenic species of Yersinia. The main activity of YadA from Y. enterocolitica is to bind collagen, and it also mediates adhesion to other molecules of the extracellular matrix. In addition, YadA is involved in serum resistance, phagocytosis resistance, binding to epithelial cells and autoagglutination. YadA is an essential virulence factor of Y. enterocolitica, and removal of this protein from the bacteria leads to avirulence. In this study, I investigated the YadA-collagen interaction by studying the binding of YadA to collagen-mimicking peptides by several biochemical and biophysical methods. YadA bound as tightly to the triple-helical model peptide (Pro-Hyp-Gly)10 as to native collagen type I. However, YadA failed to bind a similar peptide that does not form a collagenous triple helix. As (Pro-Hyp-Gly)10 does not contain a specific sequence, we concluded that a triple-helical conformation is necessary for YadA binding, but no specific sequence is required. To further investigate binding determinants for YadA in collagens, I examined the binding of YadA to a library of collagen-mimicking peptides that span the entire triple-helical sequences of human collagens type II and type III. YadA bound promiscuously to many but not all peptides, indicating that a triple-helical conformation alone is not sufficient for binding. The high-binding peptides did not share a clear binding motif, but these peptides were rich in hydroxyproline residues and contained a low number of charged residues. YadA thus binds collagens without sequence specificity. This strategy of promiscuous binding may be advantageous for pathogenic bacteria. The Eib proteins from Escherichia coli are immunoglobulin (Ig)-binding homologues of YadA. I showed conclusively that recombinant EibA, EibC, EibD and EibF bind to IgG Fc. I crystallised a fragment of the passenger domain of EibD, which binds IgA in addition to IgG. The structure has a YadA-like head domain and an extended coiled-coil stalk. The top half of the coiled-coil is right-handed with hendecad periodicity, whereas the lower half is a canonical left-handed coiled-coil. At the transition from right- to left-handedness, a small β-sheet protrudes from each monomer. I was able to map the binding regions for IgG and IgA using truncations and site-directed mutagenesis to the coiled-coil stalk and identified residues critical for Ig binding.

Stress responses of Gram-positive bacteria to cationic antimicrobial peptides

As the resistance of bacteria to conventional antibiotics has become an increasing problem, new antimicrobial drugs are urgently needed. One possible source of new antibacterial agents is a group of cationic antimicrobial peptides (CAMPs) produced by practically all living organisms. These peptides are typically small, amphipathic and positively charged and contain well defined a-helical or b-sheet secondary structures. The main antibacterial action mechanism of CAMPs is considered to be disruption of the cell membrane, but other targets of CAMPs also exist. Some bacterial species have evolved defence mechanisms against the harmful effects of CAMPs. One of the most effective defence mechanisms is reduction of the net negative charge of bacterial cell surfaces. Global analysis of gene expression of two Gram-positive bacteria, Bacillus subtilis and Staphylococcus aureus, was used to further study the stress responses induced by different types of CAMPs. B. subtilis cells were treated with sublethal concentrations of a-helical peptide LL-37, b-sheet peptide protegrin 1 or synthetic analogue poly-L-lysine, and the changes in gene expression were studied using DNA macroarrays. In the case of S. aureus, three different a-helical peptides were selected for the transcriptome analyses: temporin L, ovispirin-1 and dermaseptin K4-S4(1-16). Transcriptional changes caused by peptide stress were examined using oligo DNA microarrays. The transcriptome analysis revealed two main cell signalling mechanisms mediating CAMP stress responses in Gram-positive bacteria: extracytoplasmic function (ECF)sigma factors and two-component systems (TCSs). In B. subtilis, ECF sigma factors sigW and sigM as well as TCS LiaRS responded to the cell membrane disruption caused by CAMPs. In S. aureus, CAMPs caused a similar stress response to antibiotics interfering in cell wall synthesis, and TCS VraSR was strongly activated. All of these transcriptional regulators are known to respond to several compounds other than CAMPs interfering with cell envelope integrity, suggesting that they sense cell envelope stress in general. Among the most strongly induced genes were yxdLM (in B. subtilis) and vraDE (in S. aureus) encoding homologous ABC transporters. Transcription of yxdLM and vraDE operons is controlled by TCSs YxdJK and ApsRS, respectively. These TCSs seemed to be responsible for the direct recognition of CAMPs. The yxdLM operon was specifically induced by LL-37, but its role in CAMP resistance remained unclear. VraDE was proven to be a bacitracin transporter. We also showed that the net positive charge of the cell wall affects the signalrecognition of different TCSs responding to cell envelope stress. Inactivation of the Dlt system responsible for the D-alanylation of teichoic acids had a strong and differential effect on the activity of the studied TCSs, depending on their functional role in cells and the stimuli they sense.