The work presented in this thesis deals with the structural and functional properties of peptides at surfaces. The interaction of peptides with surfaces is an ever so common occurrence in our every day life, from the bug squashed on the windshield of our car to the barnacle on our boat, and from the blood plasma used in the hospital to the proteins in our cells. The effect these occurrences has on our lives is diverse, the bug is annoying whereas the barnacle settlement of ship hull is costly for marine transportation, the blood plasma contains components of vital importance for our immunological defense system and the proteins in our cells are crucial for regulatory processes and life.One part of this thesis, performed as a part of the EU-founded project AMBIO, deals with the concept of marine biofouling. A number of short peptides have been designed, synthesized, and used to investigate their effect on the settlement on marine biofoulers, such as the Ulva linza algae and the Navicula diatom, on template surfaces coated with thin layers of these molecules. The surfaces have been thoroughly investigated with respect of their physio-chemical properties before and after submersion in artificial seawater and ultimately in suspensions containing the organisms. The most interesting results were obtained with an arginine-rich peptide coating that when introduced to Ulva linza zoospores, displayed extensive settlement, compared to reference surfaces. In addition, a large fraction of the settled spores had an abnormal morphology.The other part of this thesis is focused on designed peptides that when adsorbed on a negatively charged surface adopts a well-defined secondary structure, either α-helical or β-sheet. Precisely placed amino acids in the peptides will strongly disfavor structure in solution, primarily due to electrostatic repulsion, but when the peptides are adsorbed on the negatively charged surfaces, they adopt a well-defined secondary structure due to ion pair bonding. These interactions have been thoroughly investigated by systematic variations of the side-chains. In order to determine the factors contributing to the induced structure, several peptides with different amino acid sequences have been synthesized. Factors that have been investigated include 1) the positive charge density, 2) distribution of positive charges, 3) negative charge density, 4) increasing hydrophobicity, and 5) incorporating amino acids with different helix propensities. Moreover, pH dependence and the effect of different interaction partners have also been investigated. It has also been shown that the system can be modified to incorporate a catalytic site that is only active when the helix is formed. This research will increase our understanding of peptide-surface interactions and might be of importance for both bionanotechnology and medicine.

Cooling water systems are needed to dissipate heat. The mist from open system cooling towers has been implicated as a source of infections of Legionella pneumophila. As a result biocide is added to cooling water systems, but the addition of biocide worsens biofouling, scaling and corrosion. Increasing environmental pressure has resulted in a move away from biocides which are usually chlorine based chemicals, so that the use of ozone instead has recently been reported as a way of controlling microbiological growth. This study aims to compare the corrosion rates (using calculated and measured surface areas) of different metals exposed to chemically treated and ozone treated cooling water in an industrial cooling water system. The types of corrosion were also observed and recorded. The scales from different components of the cooling systems as well as scale from chemically and ozone treated D tower water were characterized qualitatively using X-ray diffraction (XRD), Thermo gravimetric Analysis (TGA) and Atomic Absorption Spectroscopy. The D tower is a cooling water circuit in which the cooling water is from the Vaal River. As expected, the stainless steel has the lowest corrosion rate of 0.000 milli inches/year followed by brass with 1.531 milli inches/year and lastly mild steel (2.098 milli inches/year). Water quality rather than the presence or absence of ozone determines the corrosion rate. This confirms the findings reported in the literature. Scale from chemically treated water contains many different compounds while scale from ozone treated contains only different polymorphs of CaCO3, which is present in the water source and magnesium calcite.

Biofouling is a major issue in applying nanofiltration and reverse osmosis technologies for wastewater treatment. Biofilm formed on the surface of membranes will severely decline the flux and cause energy waste. In this study, a novel biofouling control method that applies D-amino acids to inhibit biofilm formation was investigated. The D-amino acids previously reported to inhibit biofilm formation and disrupt existing biofilm – D-tyrosine and the mixture of D-tyrosine, D-tryptophan, D-leucine and D-methionine were tested. Pseudomonas aeruginosa and Bacillus subtilis were used as model Gram-negative and Gram-positive bacteria, respectively. D-amino acids have little effect and some effect on inhibition of biofilm formation and disruption of exiting biofilm to Pseudomonas aeruginosa, but have good effect to Bacillus subtilis. A commonly used microtiter plate assay for quantitative biofilm measurement was systematically evaluated and optimized for screening biofilm control agents. The effect of D-tyrosine on inhibition of organic fouling and P. aeruginosa biofouling on NF90 membrane surface in bench scale dead end filtration experiment was examined, which shows that D-tyrosine can effectively inhibit organic fouling and P. aeruginosa biofouling on NF90 membrane surface.

Biofouling, or the formation of biofilm on membrane surfaces, can decrease the performance (decreased flux and/or increased operating pressure) of a reverse osmosis (RO) membrane system in a water treatment plant. However, biofilms have been used in water treatment systems to remove organic carbon from water via biofilters and successfully reduce biofilm growth downstream. This research investigates the possibility that the heterotrophic biofilm present on membrane surfaces removes nutrients from the treatment water, thereby making it nutrient deprived as it travels along the treatment train. This may potentially be exploited as an in situ biofilter to actively remove dissolved organic carbon (DOC) from the treatment water, thereby protecting downstream membrane surfaces from biofouling. Analysis of fouled membranes from the Dunedin water treatment plant in Dunedin, FL indicates the presence of biofilm on membrane surfaces in a gradient pattern with a higher level of fouling at the front of the element. Additionally, the community structure of the biofilm at the front of the element is unique with respect to the feed-water and downstream membrane material. Additionally, a carbon (and nitrogen) mass balance study was performed at the water treatment plant in Dunedin, FL through extensive sampling of DOC at multiple locations of the RO membrane system over a 20 month period. Plant-level mass balance results indicate a significant pool of DOC was consistently unaccounted for, and presumably assimilated or otherwise removed within the membrane system. Sampling also indicated a removal of total nitrogen. Additionally, the specific UV absorbance (SUVA) of the DOC in concentrate was consistently greater than that of the feed water, suggesting the removal of labile aliphatic carbon as the feed water travels through the feed channel of the membrane system. A pilot system was designed and built to operate under plant conditions (flow rate and pressure) to test if the biofilm on the surface of the membrane can have a protective effect for downstream membrane material. A fouled membrane element was pulled from the plant at the same time and general location as an autopsied element (to determine composition on the surface) and used in the pilot system. Feed and concentrate water from the pilot was directed to flat sheet modules for performance testing and surface characterization. This allowed for characterization of the two sections without disturbing the membrane element. Differences in performance and foulant deposition were characterized for the two sections as a function of carbon addition and flow rate. The results from this testing suggest the membrane element, or the biofilm on its surface, has both a performance and a foulant deposition benefit for downstream membranes as compared to feed membrane material. This benefit also displayed an increasing trend as the concentration of organic carbon fed into the system increases.

Surface acoustic wave (SAW) devices find uses in a plethora of applications including but not limited to chemical, biological sensing, and microfluidic actuation. The primary aim of this dissertation is to develop a SAW biosensor, capable of simultaneous detection of target biomarkers in fluid media at concentrations of picogram/ml to nanogram/ml levels and removal of non-specific proteins from sensor surface using the process of acoustic streaming, for potential chemical sensing, medical, and clinical diagnostic applications. The focus is on the development of three dimensional finite element structural and fluid-structure interaction models to study wave propagation and acoustic actuation of fluids in a SAW biosensor. This work represents a significant improvement in understanding fluid flow over SAW devices, over the currently available continuum model of Nyborg. The developed methodology includes use of a novel substrate, namely, Langasite coupled with various combinations of novel multidirectional interdigital transducer (IDT) configurations such as orthogonal, focused IDTs as well as sensor surface modifications, such as micro-cavities. The current approach exploits the capability of the anisotropic piezoelectric crystal to launch waves of different characteristics in different directions, which can be put to the multiple uses including but not limited to sensing via shear horizontal waves and biofouling elimination via Rayleigh wave induced acoustic streaming. Orthogonal IDTs gives rise to constructive interference, thereby enhancing the magnitudes of device displacements and fluid velocities. The net effect is an increase in device sensitivity and acoustic streaming intensity. The use of micro-cavities in the delay path provides a synergistic effect, thereby further enhancing the device sensitivity and streaming intensity. Focused IDTs are found to enhance the device displacements and fluid velocities, while focusing the device displacements and fluid motion at the device focal point, thereby enhancing the SAW device biosensing performance. The work presented in this dissertation has widespread and immediate use for enhancing sensor sensitivity and analyte discrimination capabilities as well as biofouling removal in medical diagnostic applications of SAW sensors. This work also has a broad relevance to the sensing of multiple biomarkers in medical applications as well as other technologies utilizing these devices such as microfluidic actuation.

Microbial colonization on the surface of silicone rubber high voltage outdoor insulators often results in the formation of highly hydrated biofilm that influence the surface properties, such as surface hydrophobicity. The loss of hydrophobicity might lead to dry band formation, and, in the worst cases, flashover and failure of the insulator. In this work, the biocidal effects of various antimicrobial compounds in silicone rubber materials were determined. These materials were evaluated according to an ISO standard for the antimicrobial activity against the growth of aggressive fungal strains, and microorganisms that have been found colonizing the surfaces of outdoor insulators in several areas in the world. Several compounds suppressed microbial growth on the surfaces of the materials without compromising the material properties of the silicone rubber. A commercial biocide and thymol were very effective against fungal growth, and sodium benzoate could suppress the fungal growth to some extent. Thymol could also inhibit algal growth. However, methods for preservation of the antimicrobial agents in the bulk of the material need to be further developed to prevent the loss of the compounds during manufacturing. Biofilm formation affected the surface hydrophobicity and complete removal of the biofilm was not achieved through cleaning. Surface analysis confirmed that traces of microorganisms were still present after cleaning. Further, surface modification of the silicone rubber was carried out to study how the texture and roughness of the surface affect biofilm formation. Silicone rubber surfaces with regular geometrical patterns were evaluated to determine the influence of the surface texture on the extent of microbial growth in comparison with plane silicone rubber surfaces. Silicone rubber nanocomposite surfaces, prepared using a spray-deposition method that applied hydrophilic and hydrophobic nanoparticles to obtain hierarchical structures, were studied to determine the effects of the surface roughness and improved hydrophobicity on the microbial attachment. Microenvironment chambers were used for the determination of microbial growth on different modified surfaces under conditions that mimic those of the insulators in their outdoor environments. Different parts of the insulators were represented by placing the samples vertically and inclined. The microbial growth on the surfaces of the textured samples was evenly distributed throughout the surfaces because of the uniform distribution of the water between the gaps of the regular structures on the surfaces. Microbial growth was not observed on the inclined and vertical nanocomposite surfaces due to the higher surface roughness and improved surface hydrophobicity, whereas non-coated samples were colonized by microorganisms. / <p>QC 20151002</p>

<p>There are over 30 million Foley urinary catheters used annually, and the greatest problem with Foley catheters is catheter-associated urinary tract infections (CAUTIs). CAUTIs are the number one cause of hospital-acquired infections and make up to 40% of nosocomial infections. Biofilms on urinary catheters are critical to the progression of symptomatic CAUTIs, but are difficult to treat due to the protective effect of the biofilm matrix against antibiotics. The anti-fouling catheter technology proposed and demonstrated herein uses a mechanical, non-antibiotic approach to physically remove biofilms and thereby provide an appealing option for potentially stopping the progression of symptomatic infections. Additionally, because the anti-fouling technology is mechanical, it can circumvent the persistent failings of chemical and biological approaches that have failed to address catheter-associated urinary tract infections for the last 50+ years since Foley catheters were introduced. </p><p>We designed and optimized urinary catheter prototypes capable of on-demand removal of biofilms from the previously-inaccessible main drainage lumen of catheters. The concept uses pressure-actuated chambers in elastomer constructs to generate regio-selective strain and thereby remove biofilms. We first grew mature Proteus mirabilis crystalline biofilms on flat silicone elastomer substrates, and showed that application of strain to the substrate debonded the biofilm, and that increasing the strain rate increased biofilm detachment. A quantitative relationship between the applied strain rate and biofilm debonding was found through an analysis of the biofilm segment length and the calculated driving force for debonding. We then constructed proof-of-concept prototypes of sections of anti-fouling catheter shafts using silicone and 3D printed reverse molding in methods akin to those used for soft robotics. The proof-of-concept prototypes demonstrated release of mature P. mirabilis crystalline biofilms from their strained surfaces, and prompted our development of more advanced multi-lumen prototypes. The multi-lumen prototypes were designed and optimized using successive rounds of finite element modeling to adjust the number and postion of intra-wall inflation lumens. We then constructed prototypes based on the optimized design with clinically relevant dimensions and showed they were able to generate greater than 30% strain on the majority of the luminal surface, and along their full length. Those catheter prototypes were able to on-demand, and repeatedly, remove greater than 80% of a mixed community biofilm of P. mirabilis and E. coli. In summary, this study shows (1) strain in the elastomeric substrate actively debonds crystalline biofilms in vitro (2) modeling based on characterization of biofilm properties and understanding of substrate strain informs and facilitates prototype catheter design (3) urinary catheter prototypes utilizing inflation-induced substrate strain are capable of on-demand and repeatedly removing biofilms in vitro.</p> / Dissertation

Dans le milieu marin, toute surface immergée est rapidement colonisée par des bactéries, puis par d'autres micro-organismes, conduisant à la formation de structures tridimensionnelles complexes appelées biofilms. Cette étape est généralement suivie par l'installation de macro-colonisateurs. Néanmoins, un certain nombre d'organismes marins, tels que les macro-algues, présentent des surfaces peu épiphytées à l'échelle macroscopique. Des algues méditerranéennes (Taonia atomaria et Dictyota spp.) ont été sélectionnées dans le cadre de ces travaux de thèse pour leur capacité à conserver leur surface peu colonisée. Cependant, des observations de leurs surfaces par microscopie ont montré l'existence de biofilms diversifiés à la surface de leurs thalles. Le but de cette thèse est de mieux comprendre les mécanismes de médiation chimique entre ces algues et les bactéries associées à leur surface. La première partie de ce travail a été consacrée à l'étude du rôle de molécules d'origine algale vis-à-vis de l'adhésion de bactéries marines. Pour cela, la composition chimique totale des algues sélectionnées a été analysée conduisant à l'isolement et à la caractérisation structurale de 12 molécules, dont trois se sont révélées être originales. L'activité anti-adhésion de la majorité de ces composés a ensuite été évaluée : le 1-O-octadecenoylglycérol s'est avéré être le produit le plus actif (20 µM < CE50 <55 µM). La deuxième partie a été dédiée plus particulièrement à l'étude du métabolome de surface de T. atomaria dans le but d'évaluer son implication dans les interactions écologiques entre l'algue et les bactéries associées à sa surface. Un protocole d'obtention et d'analyse spécifique des extraits surfaciques a tout d'abord été développé. Ce protocole est basé sur le trempage des thalles dans des solvants organiques et un contrôle de l'intégrité des cellules membranaires des algues y est associé. L'échantillonnage a été effectué mensuellement à Carqueiranne (Nord-ouest de la Méditerranée, France) durant la période allant de février à juillet 2013. Les résultats obtenus montrent qu'un sesquiterpène est exprimé majoritairement à la surface de l'algue. Il a été démontré que ce composé inhibe l'adhésion de souches bactériennes de référence tout en restant inactif vis-à-vis de celles isolées à la surface de l'algue. Une telle spécificité n'a pas été observée ni dans le cas de biocides commerciaux, ni pour les autres métabolites produits par T. atomaria. Dans un second temps, un suivi saisonnier des extraits de surface ainsi que des communautés bactériennes associées a été effectué par métabolomique (LC-MS) et DGGE, respectivement. Des fluctuations saisonnières de ces deux paramètres ont été reportées sans mettre en évidence de corrélation évidente entre eux. La présence de la molécule majeure de surface durant tout le suivi saisonnier a été notée ainsi que sa capacité à diffuser dans l'eau de mer. Enfin, l'étude de l'implication potentielle des bactéries associées à T. atomaria dans le contrôle du biofilm a été entreprise en évaluant l'activité de leurs extraits vis-à-vis de l'adhésion de souches de référence. En conclusion, nous émettons l'hypothèse que T. atomaria pourraient contrôler partiellement le biofilm associé à sa surface en faisant intervenir des métabolites spécifiques.

<p>bold</p> / Dissertation

abstract: The aims of this project are to demonstrate the design and implementation of separations modalities for 1) in situ product recovery and 2) upstream pretreatment of toxic feedstocks. Many value-added bioproducts such as alcohols (ethanol and butanol) developed for the transportation sector are known to be integral to a sustainable future. Likewise, bioproduced aromatic building blocks for sustainable manufacturing such as phenol will be equally important. The production of these compounds is often limited by product toxicity at 2- 20 g/L, whereas it may desirable to produce 20-200 g/L for economically feasible scale up. While low-cost feedstocks are desirable for economical production, they contain highly cytotoxic value-added byproducts such as furfural. It is therefore desirable to design facile detoxification methods for lignocellulose-derived feedstocks to isolate and recover furfural preceding ethanol fermentation by Escherichia coli. Correspondingly it is desirable to design efficient facile in situ recovery modalities for bioalcohols and phenolic bioproducts. Accordingly, in-situ removal modalities were designed for simultaneous acetone, butanol, and ethanol recovery. Additionally, a furfural removal modality from lignocellulosic hydrolysates was designed for upstream pretreatment. Solid-liquid adsorption was found to serve well each of the recovery modalities characterized here. More hydrophobic compounds such as butanol and furfural are readily recovered from aqueous solutions via adsorption. The primary operational drawback to adsorption is adsorbent recovery and subsequent desorption of the product. Novel magnetically separable mesoporous carbon powders (MMCPs) were characterized and found to be rapidly separable from solutions at 91% recovery by mass. Thermal desorption of value added products was found efficient for recovery of butanol and furfural. Fufural was desorbed from the MMCPs up to 57% by mass with repeated adsorption/thermal desorption cycles. Butanol was recovered from MMCPs up to an average 93% by mass via thermal desorption. As another valuable renewable fermentation product, phenol was also collected via in-situ adsorption onto Dowex Optipore L-493 resin. Phenol recovery from the resins was efficiently accomplished with tert-butyl methyl ether up to 77% after 3 washes. / Dissertation/Thesis / Doctoral Dissertation Chemical Engineering 2017