Research toward a multiplexed nucleic acid biosensor that uses quantum dots (QDs) as donors in a fluorescence resonance energy transfer (FRET) assay is described. Optical fibers were modified with mixed films composed of different colours of QDs and different oligonucleotide probes that served as scaffolds for the hybridization of the corresponding target nucleic acid sequences. Fluorescent dyes that were suitable as acceptors for each QD donor were associated with hybridization and provided an analytical signal through FRET-sensitized emission. Different detection channels were achieved through the combination of different donors and acceptors: green emitting QDs with Cyanine 3 or Rhodamine Red-X; and red emitting QDs with Alexa Fluor 647. A detection channel that used the direct excitation of Pacific Blue complemented the FRET pairs. One-plex, two-plex, three-plex and four-plex hybridization assays were demonstrated. A sandwich assay format was adopted to avoid target labeling. Detection limits were 1-10 nM (1-12 pmol) and analysis times were 1-4 h. Single nucleotide polymorphisms were discriminated in multiplexed assays, and the potential for reusability was also demonstrated. Non-selective interactions between QDs and oligonucleotides were characterized, and routes toward the optimization of the QD-FRET hybridization assays were identified. A basic model for multiple FRET pathways in a mixed film was also developed. In addition to the advantages of solid-phase assays, the combination of QDs and FRET was advantageous because it permitted multiplexed detection using a single excitation source and a single substrate, in the ensemble, and via ratiometric signals. Spatial registration or sorting methods, imaging or spatial scanning, and single molecule spectroscopy were not required. The research in this thesis is expected to enable new chip-based biosensors in the future, and is an original contribution to both bioanalytical spectroscopy and the bioanalytical applications of nanomaterials.

The main project Dry preservation of source-separated organic household wastes involves a new technique for treatment of biowaste through drying. Investigations are going on to determine how the dried biowaste best can be used to close the natural circular flow of nutrients. The objective of this degree project is to determine if the dried biowaste can be used as a soil conditioner. By restoring the nutrients in the material to the ground, the natural circular flow is closed. A declaration of contents, including the nutrient levels, C/N ratio, pH and the electrical conductivity of the dried biowaste, was constructed and a germination test was done to make sure that the material did not inhibit sprouting. Further on a method was developed to study the decomposition process, and in particular the nitrogen mineralization of the dried biowaste. This method was then used practically. The results of this degree project indicate that the decomposition capacity of the dried biowaste is very good. The germination test showed that the material in a diluted form (up to 50 % dried biowaste) did not inhibit sprouting. The examination of the nitrogen mineralization showed a fast liberalisation of nutrients available to plants, with only a shorter period of nitrogen immobilization. Together these results imply that the dried material could function well as a soil conditioner. / Projektet Torrkonservering av matavfall från hushåll innefattar en helt ny teknik för behandling av bioavfall genom torkning. Undersökningar pågår angående hur det torkade bioavfallet bäst kan användas för att sluta det naturliga kretsloppet. Examensarbetets huvudsyfte var, som ett led i dessa undersökningar, att utreda om det torkade bioavfallet kan användas som ett jordförbättringsmedel. Genom att tillföra bioavfallet till jord så återförs näringen i materialet till marken och kretsloppet sluts. En varudeklaration, med materialets näringshalter, C/N-kvot, pH och elektrisk konduktivitet, togs fram och ett groningstest utfördes för att kontrollera att bioavfallet inte var groningshämmande. Vidare utvecklades en metod för att studera det torkade bioavfallets nedbrytningsegenskaper i form av dess kvävemineralisering. Denna metod användes därefter praktiskt. Resultatet av detta examensarbete tyder på att torkat bioavfall har mycket goda nedbrytningsegenskaper. Groningsförsöket visade att materialet i utspädd form (upp till 50 % torkat bioavfall) inte är groningshämmande, och mineraliseringsförsöket visade på en snabb frigörelse av växttillgängligt kväve, och en immobiliseringsperiod på ett par veckor. Tillsammans indikerar dessa resultat att det torkade materialet kan fungera väl som ett jordförbättringsmedel.

Research toward a multiplexed nucleic acid biosensor that uses quantum dots (QDs) as donors in a fluorescence resonance energy transfer (FRET) assay is described. Optical fibers were modified with mixed films composed of different colours of QDs and different oligonucleotide probes that served as scaffolds for the hybridization of the corresponding target nucleic acid sequences. Fluorescent dyes that were suitable as acceptors for each QD donor were associated with hybridization and provided an analytical signal through FRET-sensitized emission. Different detection channels were achieved through the combination of different donors and acceptors: green emitting QDs with Cyanine 3 or Rhodamine Red-X; and red emitting QDs with Alexa Fluor 647. A detection channel that used the direct excitation of Pacific Blue complemented the FRET pairs. One-plex, two-plex, three-plex and four-plex hybridization assays were demonstrated. A sandwich assay format was adopted to avoid target labeling. Detection limits were 1-10 nM (1-12 pmol) and analysis times were 1-4 h. Single nucleotide polymorphisms were discriminated in multiplexed assays, and the potential for reusability was also demonstrated. Non-selective interactions between QDs and oligonucleotides were characterized, and routes toward the optimization of the QD-FRET hybridization assays were identified. A basic model for multiple FRET pathways in a mixed film was also developed. In addition to the advantages of solid-phase assays, the combination of QDs and FRET was advantageous because it permitted multiplexed detection using a single excitation source and a single substrate, in the ensemble, and via ratiometric signals. Spatial registration or sorting methods, imaging or spatial scanning, and single molecule spectroscopy were not required. The research in this thesis is expected to enable new chip-based biosensors in the future, and is an original contribution to both bioanalytical spectroscopy and the bioanalytical applications of nanomaterials.

Although enzymes show great potential for use in industrial applications, their implementation from a practical perspective is still somewhat limited by various shortcomings in the area of enzyme immobilization. The use of silica sol-gels for protein entrapment has been studied extensively over the past 15 years or so. However, our understanding of the interactions between the immobilization matrix and the entrapped biomolecules is still relatively poor. Non-invasive in situ spectroscopic characterization is a promising approach to gain a better understanding of the fundamentals governing sol-gel immobilization. This thesis describes the application of Fourier transform infrared (FTIR) microscopy, two dimensional (2D) FTIR and fluorescence spectroscopy to characterize the immobilization matrix, entrapped model proteins and their interactions. Hydroperoxide lyase (HPL [E.C. 4.1.2.]) was chosen as a potential model protein for sol-gel entrapment. HPL activity was evaluated by use of factorial experimental design investigating the effects of KCl and Triton X-100 on HPL activity with 13-hydroperoxy-octadecadienoic acid (LA-OOH) and the novel water soluble 13-hydroperoxy-octadienoyl sulfate (LS-OOH) as substrates. The highest HPL activity was achieved under aqueous conditions with high salt and low surfactant concentrations and LA-OOH as the substrate. A significant interaction between salt and surfactant as well as salt and substrate was identified and a hypothesis to explain the basis of the interaction phenomena is presented. To analyze sol-gels with spectroscopic techniques, a sample format amenable to these techniques was needed. Therefore, a spin-coating technique for the preparation of aluminum or glass supported sol-gel thin films containing immobilized protein and a varying degree of the organically modified precursor propyltrimethoxysilane (PTMS) was developed. This approach produced samples that were suitable for chemical mapping using FTIR microscopy or fluorescence spectroscopic investigations. A data analysis method was developed to extract information on chemical speciation and distribution from FTIR data matrices obtained through FTIR microscopy. Results indicate that sol-gel thin films are not homogeneous on the microscopic level. Instead, they are heterogeneous with a clustering in the distribution of the model proteins studied (lysozyme [E.C. 3.2.1.17], lipase [E.C. 3.1.1.3] and bovine serum albumin (BSA)) at the scale investigated. The appearance of these clusters was found to depend on the type of protein entrapped, as well in some cases on the composition of the sol-gel. Moreover, the PTMS distribution was positively correlated with the protein distribution in the case of lipase and negatively correlated in the case of lysozyme and BSA. Additionally, sol-gels with a higher PTMS content appeared to conserve protein structure in areas where lipase clustered. Lysozyme and BSA, on the other hand, seemed to retain their structures in high concentration clusters better at lower PTMS content. A hypothesis taking into account the surface hydrophobicity of the proteins and the sol-gel composition as the basis for these phenomena is proposed. Fluorescence spectroscopy revealed that the PTMS content of the sol-gels had a direct effect on the physical properties of the immobilized proteins as evidenced by a blue shift of the intrinsic tryptophan (TRP) fluorescence. Temperature-dependent fluorescence spectroscopy revealed that the amount of TRP quenching was inversely proportional to the PTMS content of the sol-gel, suggesting that there were varying amounts of water available for quenching for the different immobilized enzyme systems. Analysis of the sol-gels by 2D FTIR spectroscopy with a focus on the amide A region using Gaussian peak deconvolution revealed two different species of water for the 50 % PTMS thin film sol-gels with BSA that could be described as fully and not fully H-bonded. It was also found that these species of water showed different removal profiles during thermal treatment. 2D FTIR of the amide I region followed by absorbance difference spectrum evaluation revealed that the temperature stability of the three model proteins was also sol-gel composition dependent. A hypothesis that the surface characteristics of the proteins determine the nature of the composition dependence is presented.

Although enzymes show great potential for use in industrial applications, their implementation from a practical perspective is still somewhat limited by various shortcomings in the area of enzyme immobilization. The use of silica sol-gels for protein entrapment has been studied extensively over the past 15 years or so. However, our understanding of the interactions between the immobilization matrix and the entrapped biomolecules is still relatively poor. Non-invasive in situ spectroscopic characterization is a promising approach to gain a better understanding of the fundamentals governing sol-gel immobilization. This thesis describes the application of Fourier transform infrared (FTIR) microscopy, two dimensional (2D) FTIR and fluorescence spectroscopy to characterize the immobilization matrix, entrapped model proteins and their interactions. Hydroperoxide lyase (HPL [E.C. 4.1.2.]) was chosen as a potential model protein for sol-gel entrapment. HPL activity was evaluated by use of factorial experimental design investigating the effects of KCl and Triton X-100 on HPL activity with 13-hydroperoxy-octadecadienoic acid (LA-OOH) and the novel water soluble 13-hydroperoxy-octadienoyl sulfate (LS-OOH) as substrates. The highest HPL activity was achieved under aqueous conditions with high salt and low surfactant concentrations and LA-OOH as the substrate. A significant interaction between salt and surfactant as well as salt and substrate was identified and a hypothesis to explain the basis of the interaction phenomena is presented. To analyze sol-gels with spectroscopic techniques, a sample format amenable to these techniques was needed. Therefore, a spin-coating technique for the preparation of aluminum or glass supported sol-gel thin films containing immobilized protein and a varying degree of the organically modified precursor propyltrimethoxysilane (PTMS) was developed. This approach produced samples that were suitable for chemical mapping using FTIR microscopy or fluorescence spectroscopic investigations. A data analysis method was developed to extract information on chemical speciation and distribution from FTIR data matrices obtained through FTIR microscopy. Results indicate that sol-gel thin films are not homogeneous on the microscopic level. Instead, they are heterogeneous with a clustering in the distribution of the model proteins studied (lysozyme [E.C. 3.2.1.17], lipase [E.C. 3.1.1.3] and bovine serum albumin (BSA)) at the scale investigated. The appearance of these clusters was found to depend on the type of protein entrapped, as well in some cases on the composition of the sol-gel. Moreover, the PTMS distribution was positively correlated with the protein distribution in the case of lipase and negatively correlated in the case of lysozyme and BSA. Additionally, sol-gels with a higher PTMS content appeared to conserve protein structure in areas where lipase clustered. Lysozyme and BSA, on the other hand, seemed to retain their structures in high concentration clusters better at lower PTMS content. A hypothesis taking into account the surface hydrophobicity of the proteins and the sol-gel composition as the basis for these phenomena is proposed. Fluorescence spectroscopy revealed that the PTMS content of the sol-gels had a direct effect on the physical properties of the immobilized proteins as evidenced by a blue shift of the intrinsic tryptophan (TRP) fluorescence. Temperature-dependent fluorescence spectroscopy revealed that the amount of TRP quenching was inversely proportional to the PTMS content of the sol-gel, suggesting that there were varying amounts of water available for quenching for the different immobilized enzyme systems. Analysis of the sol-gels by 2D FTIR spectroscopy with a focus on the amide A region using Gaussian peak deconvolution revealed two different species of water for the 50 % PTMS thin film sol-gels with BSA that could be described as fully and not fully H-bonded. It was also found that these species of water showed different removal profiles during thermal treatment. 2D FTIR of the amide I region followed by absorbance difference spectrum evaluation revealed that the temperature stability of the three model proteins was also sol-gel composition dependent. A hypothesis that the surface characteristics of the proteins determine the nature of the composition dependence is presented.

Polymeric nanoparticles are potential candidates as carriers for pharmaceutical agents. Development of such nanoparticles generally requires molecules immobilized on the particle surfaces to ensure biocompatibility and/or targeting abilities. Following particle preparation and surface modification, excess reagents must be removed. Ultracentrifugation, which is the most widely used purification technique as per today, is not feasible in industrial applications. In this diploma work, tangential flow filtration is studied as an alternative purification method which is better suited for implementation in a large-scale process. Comparison of ultracentrifugation and tangential flow filtration in diafiltration mode for purification of nanoparticles, indicate that they are comparable with respect to particle stability and the removal of the surfactant SDS from methacrylic anhydride nanoparticles. The purification efficiency of tangential flow filtration is superior to that of ultracentrifugation. Conductivity measurements of filtrates and supernatant liquids show that a stable conductivity value can be reached 6 times faster in filtration than in centrifugation with equipment and settings used. This conductivity arises from several types of molecules, and the contribution from surfactant molecules alone is not known. However, protein adsorption on the particles indicates successful removal of surfactant. Conductivity and tensiometry were evaluated as potential methods to quantify surfactant in solutions, but both proved unsatisfactory. Using bovine serum albumin as a model protein, the extent of immobilization to nanoparticles is evaluated at different pH. A maximum amount of 6,8 mg/m2 is immobilized, whereof an unknown part is covalently bound. This coverage is achieved at pH 4,0 and is probably partly due to low electrostatic repulsion between particle and protein. An estimation of 2,0 µmol covalently bound BSA per gram of nanoparticles corresponds to 5,3 mg/m2 and a surface coverage of 76%. Removal of excess reagents after surface modification is done with ultracentrifugation instead of filtration, as particle aggregates present after the immobilization reaction might foul the membrane.

Effective vascularization is crucial for almost any therapeutic tissue engineering concept. In this context, therapeutic angiogenesis attempts to enforce the natural process of blood vessel formation by provision of bioactive effectors. Along these lines, the aim of this work was to evaluate the potential of a modular hydrogel composed of the synthetic star-shaped poly(ethylene glycol) (starPEG) and the naturally occurring biopolymer heparin for the defined and orchestrated delivery of two major angiogenic growth factors, fibroblast growth factor-2 (FGF-2) and vascular endothelial growth factor (VEGF). While starPEG determines the structural properties of the gel materials, effective administration of both cytokines is based on their natural affinity to heparin, the highly charged polysaccharidic building block capable of reversibly binding various growth factors upon geometrically matching electrostatic interactions. Varying the molar ratio of starPEG to heparin upon network formation, different hydrogel types with distinct mechanical characteristics but constant heparin content could be produced. As heparin represents the basis for the growth factor interaction with the scaffolds, the matrices were found to bind and release FGF-2 or VEGF independently of the particular network stiffness and structural properties of the different gel types. Moreover, the material could be utilized for a modular delivery of growth factor combinations over a broad range of concentrations. To evaluate the general suitability for pro-angiogenic stimulation, the provision of FGF-2 and VEGF from starPEG-heparin hydrogels differing in their mechanical characteristics and biofunctionalization with adhesive peptides was studied using human endothelial cells, the cell type that forms the inner layer of any blood vessel. Results showed that the presence of the adhesion ligand was an essential requirement to mediate cell attachment and subsequent growth on the scaffolds. Apart from that, hydrogels with an intermediate stiffness showed beneficial effects on endothelial cell proliferation/survival while in parallel also the differentiation into elongated, pro-tubular structures could be promoted. While the delivery of FGF-2 was able to enhance cell growth, VEGF mainly initiated endothelial cell shape elongation. However, with a parallel administration of both growth factors, their beneficial effects could be combined to obtain high numbers of endothelial cells undergoing differentiation. Furthermore, besides the possibility of growing endothelial cells on top of the biofunctionalized hydrogels, the release of growth factors by starPEG-heparin matrices could be applied as a stimulus to attract the cells to migrate into the direction of the scaffolds. While FGF-2 and VEGF supported cell motility to a similar extent, their combined action was found to exert the strongest effect on endothelial cell migration. Based on the results of these in vitro experiments, matrices most effectively stimulating pro-angiogenic cellular responses were selected for in vivo studies applying the functionalized materials to the chorioallantoic membrane (CAM) of fertilized chicken eggs, an assay commonly used to evaluate the vascularization potential of biomaterials. In this assay, the delivery of FGF-2 and/or VEGF by starPEG-heparin hydrogels induced a substantial angiogenic response within the CAM system, while the combination of both growth factors tends to increase vascularization most effectively. In order to adjust the starPEG-heparin hydrogel system to the complex requirements of therapeutic angiogenesis, further options to specifically modulate the FGF-2 or VEGF release were explored. With the incorporation of enzymatically cleavable peptide linkers, not only the possibility for a cellular remodeling of the gel matrix could be permitted, but also the growth factor release was substantially enhanced upon network degradation. Moreover, with the gradual removal of FGF-2 and VEGF interaction sites from heparin upon selective desulfation, the binding of both growth factors to hydrogels composed out of starPEG and desulfated heparin was significantly reduced depending on the remaining sulfate content. Irrespective of the lower immobilized amounts of FGF-2 or VEGF, higher absolute quantities of both growth factors could be released and retained in the medium due to their decreased affinity to heparin, thereby enhancing the delivery efficiency of the scaffolds. Going beyond common concepts for triggered cytokine release, hydrogel-bound FGF-2 or VEGF could be effectively displaced from their heparin binding sites by an application of the competitive, highly-heparin affine molecule chitosan. As chitosan could be introduced at different time points, not only the amounts of delivered growth factor were enhanced, but also the FGF-2 or VEGF release kinetics could be specifically modulated. Taken together, starPEG-heparin hydrogels with independently adaptable physical and biomolecular composition were demonstrated to provide time-resolved multi-factor delivery of pro-angiogenic growth factors resulting in valuable new options for therapeutic angiogenesis.

<p>The goal of this work is to develop novel molecular systems, functionalization techniques, and data collection routines with which to study the binding of immobilized cognate binding partners. Our ultimate goal is the routine evaluation of thermodynamic parameters for immobilized systems through interpretation of the variation of the binary probability of binding as a function of soluble ligand concentration. The development of both data collection routines that minimize non-specific binding and functionalization techniques that produce stable ordered molecular systems on surfaces are of paramount importance towards achievement of this goal. Methodologies developed here will be applied to investigating the thermodynamics of multivalent systems.</p><p>In the first part of this work, the effect of contact force on molecular recognition force microscopy experiments was investigated. Increased contact forces (>250 pN) resulted in increased probabilities of binding and decreased blocking efficiencies for the cognate ligand-receptor pair lactose-G3. Increased contact force applied to two control systems with no known affinity, mannose-G3 and lactose-KDPG aldolase resulted in non-specific ruptures that were indistinguishable from those of specific lactose-G3 interactions. Thus, it is essential to design data collections routines that minimize contact forces to ensure that ruptures originate from specific, blockable interactions.</p><p>In the second part of this work we report the first example of the preparation of stable self assembled monolayers through hydrosilylation of a protected aminoalkene onto hydrogen-terminated silicon nitride AFM probes and subsequent conjugation with biomolecules for force microscopy studies. Our technique can be used as a general attachment technique for other molecular systems.</p><p>In the third part of this work we develop novel molecular systems for tethering oriented vancomycin and its cognate binding partner L-Lys-D-Ala-D-Ala to surfaces and AFM tips. Unbinding experiments demonstrated that traditional methods for forming low surface density amine layers (silanization with APTMS and etherification with ethanolamine) provided molecular constructs which displayed probabilities of binding that were too low and showed overall variability too high to use for probabilistic evaluation of thermodynamics parameters. Instability and heat-induced polymerization of APTMS layers on tips and surfaces also prohibited their utility. Formation of Alkyl SAMs on silicon provides a more reliable, stable molecular system anchored by Si-C bonds that facilitates attachment of vancomycin and is capable of withstanding prolonged exposure to heated organic and aqueous environments. It follows that covalent immobilization of KDADA to silicon nitride AFM tips via Si-C bonds using hydrosilylation chemistry will be similarly advantageous. These methods offer great promise for probabilistic evaluation of thermodynamic parameters characterizing immobilized binding partners and will permit unambiguous determination of the role of multivalency in ligand binding, using an experimental configuration in which intermolecular binding and aggregation are precluded.</p> / Dissertation

Iron oxide-bearing minerals have long been recognized as an effective reactive media for arsenic-contaminated groundwater remediation. This research aimed to develop a technique that could facilitate in situ oxidative precipitation of Fe3+ in a soil (sand) media for generating a subsurface iron oxide-based reactive barrier that could immobilize arsenic (As) and other dissolved metals in groundwater. A simple in situ arsenic treatment process was successfully developed for treating contaminated rural groundwater using iron oxide-coated sand (IOCS). Using imbibition flow, the system facilitated the dispersive transport of ferrous iron (Fe2+) and oxidant solutions in porous sand to generate an overlaying blanket where the Fe2+ was oxidized and precipitated onto the surface as ferric oxide. The iron oxide (FeOx) emplacement process was significantly affected by (1) the initial surface area and surface-bound iron content of the sand, (2) the pH and solubility of the coating reagents, (3) the stability of the oxidant solution, and (4) the chemical injection schedule. In contrast to conventional excavate-and-fill treatment technologies, this technique could be used to in situ replace a fresh iron oxide blanket on the sand and rejuvenate its treatment capacity for additional arsenic removal. Several bench-scale experiments revealed that the resultant IOCS could treat arsenic-laden groundwater for extended periods of time before approaching its effective life cycle. The adsorption capacity for As(III) and As(V) was influenced by (1) the amount of iron oxide accumulated on the sand surface, (2) the system pH, and (3) competition for adsorption sites from other groundwater constituents such as silicon (Si) and total dissolved solids (TDS). Although the IOCS could be replenished several times before exhaustion, the life cycle of the FeOx reactive barrier may be limited by the gradual loss of hydraulic conductivity induced by the imminent reduction of pore space over time.

ABSTRACT PREPARATION OF CROSS-LINKED TYROSINASE AGGREGATES Aytar, Burcu Selin M.S., Department of Chemical Engineering Supervisor: Prof. Dr. Ufuk Bakir June 2006, 82 pages The aim of this study was to prepare cross-linked enzyme aggregate (CLEA) from crude mushroom (Agaricus bisporus) extract. However, the optimization of CLEA production was performed by using pure tyrosinase. Important parameters were determined as protein, ammonium sulfate and glutaraldehyde concentrations, CLEA particle size, and cross-linking temperature and period. On the other hand, the order of ammonium sulfate and glutaraldehyde addition did not affect the yield of CLEA. Optimum CLEA preparation conditions were 60 % ammonium sulfate saturation, 2 % (v/v) glutaraldehyde, and 3 hour cross-linking reaction at room temperature. Particle size of the CLEAs should be reduced by mechanical stirring to eliminate mass transfer limitations. Under these circumstances, 100 % recovery was obtained from both pure and crude tyrosinases. Optimum temperature and the activation energy for catechol oxidation were determined as 34 oC and 16.9 kcal/mol for CLEAs, whereas, 32 oC and 12.5 kcal/mol for the free enzyme. Furthermore, the thermostability of CLEAs was significantly higher than the free enzyme. CLEAs, prepared from crude mushroom extract, retained 72 % of its maximum activity in eight months storage at 4 oC. Moreover, changing the storage temperature from 4 oC to room temperature did not decrease CLEAs stabilities.