Thesis (M.Sc.), Memorial University of Newfoundland, 2000. / Bibliography: leaves 115-118.

Thesis (Ph. D.)--University of Chicago, Department of Physics, December 2003. / CD-ROM includes PDF files of figures 2.1-4.7. Includes bibliographical references. Also available on the Internet.

Thesis (doctoral)--University of Lund.

Modern microbialites are carbonate-precipitating microbial mats and represent the closest living analogues to ancient stromatolites. These ancient carbonate formations are the oldest fossil evidence of life on Earth; however, our comprehension of their relationship to early earth ecosystems relies heavily on understanding the formation of modern microbialites. Research regarding these formation processes has suggested that chemical constraints of CaCO 3 precipitation vary on sub-millimeter spatial scales within the living microbial community. In an attempt to shed light on the importance of these chemical microenvironments, this study focused on understanding the spatial distribution of the organisms and processes involved in the formation of modern microbialites. This was accomplished by isolating five visually distinct layers from the upper 2 – 3 cm of an actively forming microbialite found in the freshwater system of Cuatro Ciénegas, Mexico. Each layer was analyzed using genomic, molecular organic, and stable isotopic techniques. Bacterial diversity was determined by 16S rRNA gene analyses, lipid biomarker content was detected by GC-MS, and carbon isotope composition of organic matter and CaCO 3 were used as indicators of specific microbial processes. Results of the 16S rRNA gene analysis showed that there is little overlap in the community composition of individual layers. Approximately 90% of the ribotypes identified in the microbialite were unique to a single layer. Furthermore, the relative accretion of CaCO 3 at each layer was used to connect the distribution of organisms and processes with two specific zones of CaCO 3 precipitation. The first zone of CaCO3 accretion, which accounted for approximately 55% of total CaCO 3 accumulation, is found in the surface two layers of the microbialites and dominated by photoautotrophic cyanobacteria and algae. The second zone of CaCO 3 precipitation, found at the interior (layers 4 and 5), is composed primarily of heterotrophic proteobacteria and dominated by sulfate-reducing !-proteobacteria. The lipid content of the microbialite reflected the community structure as determined by genomics. Numerous photosynthetic biomarkers were detected and decreased in abundance with depth, indicating the important function of heterotrophic degradation. Additionally, the detection of sulfurized phytol compounds in layer 5 highlighted an important mechanism for the preservation of biogenic signatures, and reflected both the abundance of phototrophic organisms and sulfatereducing bacteria. In combination, these interdisciplinary analyses provided an understanding of microbial community composition and metabolism while indicating the spatial relationship to CaCO 3 formation and the preservation of distinct biochemical signatures. !

The behavior of a protein molecule at the solid-liquid interface is a worthy scientific problem for at least three reasons. The main driving force for studying this problem is a practical one, as many areas of bio-related technologies, such as medical implants, biosensing, and drug delivery, require the understanding of protein-surface interactions. In this dissertation, the nature of the precursive weakly adsorbed state of proteins during binding is reviewed. From this perspective, the adsorption and binding of proteins to a solid block copolymer thin film was achieved with regular spacing. Further efforts produced a monolayer of green fluorescent protein (GFP) covalently bound with regular spacing and orientation to a diblock copolymer thin film. This protein could be folded and refolded by changing solvent characteristics. We also explored the binding of DC-SIGN to mannose and mannotriose bearing lipid membranes. While no binding was observed, the usefulness of the lipid-based glycan microarray was proven using the well-studied CTB-GM1 binding motif. / text

The liver maintains energy substrate homeostasis by synchronizing circadian or diurnal expression of metabolic genes with the feeding/fasting state. The activities of hepatic de novo lipogenic gene products peak during feeding, converting carbohydrates into fats that provide vital energy sources for peripheral tissues. Conversely, deregulated hepatic lipid synthesis leads to systemic metabolic dysfunction, establishing the importance of temporal regulation of fat synthesis/usage in metabolic homeostasis. Pharmacological activation of peroxisome proliferator-activated receptor \(\delta / \beta (PPAR \delta / \beta)\)improves glucose handling and systemic insulin sensitivity. However, the mechanisms of hepatic \(PPAR\delta\) actions and the molecular pathways through which it is able to modulate global metabolic homeostasis remain unclear. Here we show that hepatic \(PPAR\delta\) controls the diurnal expression of lipogenic genes in the dark/feeding cycle. Adenovirus mediated liver restricted activation of \(PPAR\delta\) promotes glucose utilization in the liver and fat utilization in the muscle. Liver specific deletion of either \(PPAR\delta\) or the \(PPAR\delta\)-regulated lipogenic gene acetyl-CoA carboxylase 1 (ACC1) reduces muscle fatty acid uptake. Unbiased metabolite profiling identifies 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC) as a serum lipid derived from the hepatic \(PPAR\delta\)-ACC1 activity that reduces postprandial lipid levels and increases muscle fatty acid uptake. These findings reveal a regulatory mechanism that coordinates lipid synthesis and utilization in the liver-muscle axis, providing mechanistic insights into the hepatic regulation of systemic energy substrates homeostasis.

This thesis describes a geographically- and temporally-resolved, integrated biological and engineering model that estimates algal biomass and lipid production under resource-limited conditions with hourly and county resolution. Four primary resources are considered in this model: sunlight, carbon dioxide, water, and land. The variation in quantity and distribution of these resources affects algae growth, and is integrated into the analysis using a Monod model of algae growth, solar insolation data, and published values for water, carbon dioxide, and land availability. Finally, lipid production is calculated by assuming oil content based on dry weight of the biomass. The model accommodates a range of growth and production scenarios, including water recycling, co-location with wastewater treatment plants and coal-fired generators, and photobioreactor type (open pond or tubular), among others. Results for every county in Texas indicate that between 86 million and 2.2 billion gallons of lipids per year can be produced statewide for the various growth scenarios. The analysis suggests that algal biomass and lipid production does indeed vary geographically and temporally across Texas. Overall, most counties are water-limited for algae production, not sunlight or carbon dioxide-limited. However, there are many nuances in biomass and lipid production by county. Counties in west Texas are typically not solar- or land-limited, but are constrained by either water or carbon dioxide resources. Consequently, counties in east Texas are limited by either water, or land (depending on the fraction of water recycling). Varying carbon dioxide concentration results in higher growth rates, but not always increased biomass and lipid production because of limitations of other resources in each county. / text

Temperature dependent optical properties of lipid tissue verify critical information of tissue dynamics which can be applied to tissue treatment and diagnosis of various pathological features. Current methods of treating lipid rich tissues via heating are associated with post operation complications. Recent studies shows potential of lipid rich tissue removal by cooling. For monitoring cooling procedure and physical and chemical changes in lipid tissue, temperature dependent optical properties in subzero cooling need to be verified. This study designed heat transfer system estimating heat flux by cooling and programmed codes for image and data processing to obtain refractive indices of rodent subcutaneous lipid tissue. Phase transition of lipid tissue was observed and finally verified temperature dependent refractive index coefficient of lipid tissue from 24°C to -10°C. / text

The work described here has focused on two types of supramolecular assemblies, supported lipid bilayers (SLBs) and giant vesicles (GVs) from polymerizable lipids. SLBs are explored extensively as structural models in biophysical studies of cell membranes and biosensor coatings. With regard to implementation as biocompatible scaffoldings for receptor-based molecular devices, fluid SLBs lack chemical, thermal and mechanical stability as lipids are self-organized by weak, noncovalent forces. One possible solution is to use synthetic lipid monomers that can be polymerized to form robust bilayers. A key question is how polymerization affects transmembrane protein structure and activity. Specifically it is unclear if lipid cross-linking can be achieved without adversely affecting the activity of incorporated proteins. In this work the effect of lipid polymerization on transmembrane protein activity was studied with rhodopsin. The protein was reconstituted into SLBs composed of polymerizable lipids, bis-SorbPC, bis-SorbPC:mono-SorbPC, bis-DenPC and bis-SorbPC:mono-SorbPE. Rhodopsin photoactivity was monitored using plasmon waveguide spectroscopy. The results show that reconstitution of rhodopsin into SLBs composed of phosphatidylcholine with the polymerizable moiety in the acyl chain terminus, followed by photoinduced cross-linking of the lipids, does not significantly perturb protein function. A possible explanation is that a bilayer with relatively low Xn retains sufficient elasticity to accommodate the membrane deformation that accompanies the conformational change associated with rhodopsin photoactivation when polymerized in the acyl chain terminus. GVs have diameters ranging from several to few hundred micrometers and thus can be observed by optical microscopic methods. This allows manipulation of individual vesicles and observation of their transformations in real time. GVs have attracted attention as microcontainers for enzymes and drugs, and as biosensors. With the aim of increasing stability for these types of applications, GVs were prepared from synthetic dienoyl lipids that can be polymerized to form robust vesicles. The stability of these vesicles after polymerization was investigated by surfactant treatment, drying and rehydration, and temperature variations. The structure of poly(GVs) was largely retained under these conditions which destroy unpolymerized vesicles. Permeability studies on poly(GVs) suggests that they could be potentially used in a variety of technological applications, including sensors, macromolecular carriers, and microreactors.

This dissertation covers a broad range of research topics all towards the ultimate goal establishing of a novel type of biosensor in which the biocompatible membrane structure reconstituted with functional transmembrane proteins is utilized as the sensing element. It focuses on 1) examining the activity of a model transmembrane protein, bovine rhodopsin (Rho) when reconstituted into stabilized lipid membranes and 2) the instrumentation of a novel type of optical spectroscopy, plasmon waveguide resonance (PWR), which is a surface sensitive technique and its application in sensing biological events.Lipid membrane play crucial roles in cell function. Their biophysical properties affect the activity of a large amount of transmembrane receptors. They are great candidates for biosensing/ biomedical coating. However, the intrinsic instability of natural or fluid membranes prevents them to be used in a device. Studies have been done to show indirect evidence that the activity of Rho maybe maintained in polymerized membrane composed of bis-SorbPC lipids. The activity of Rho reconstituted into vesicular membranes comprised of various lipids was studied by a more direct technique, UV-Vis. It was found Rho activity was maintained to 66% of that in natural Egg PC lipid in the mixture of Egg PC:(poly)bis-SorbPC (1:1 mol:mol) as opposed to minimal values in 100 % (poly)lipids.A new type of spectral PWR was developed. The working concept, technical characterization and comparisons with similar techniques were discussed and compared in this work. A modified version of angular PWR in which lipid bilayers were formed by vesicle fusion was also developed. This method excludes possible effects from a high boiling point organic solvent on either the lipid bilayer itself or the membrane proteins associated with it. A calculating program NphaseAll for PWR was developed to do predictions of waveguide properties can be made to provide guidance for waveguide design. Theoretical calculations were done for PWR and experimental results were compared with the theoretical predictions.PWR was used to detect the formation of a biological lipid membrane, the association of alpha synuclein with membranes and the binding activity of human melanarcortin to its ligands in fluid and polymerized/dried membranes.