The synthesis and breakdown of sugars is one of the most important functions in Nature. Consequently, sugar structures are used both as energy storage and as building blocks to stabilise and protect the cell. The formation of these structures is performed by glycosyltransferases (GT), an enzyme group structurally conserved within all kingdoms. Until now, only two different folds have been discovered by crystallisation of GTs, i.e. GT-A and GT-B. A third fold family has however been proposed by fold predictions. In this thesis, a multivariate data analysis was successfully used in classifying and predicting both fold and reaction mechanism (inverting or retaining) of GTs. This method was also used to obtain information about the separating parameters for the reaction mechanism classification. This information could be traced back to the amino acid sequence. The method could as well be used to analyse and identify the properties of membrane binding regions of GTs, and subsequently distinguish soluble from membrane-associated enzymes. Most functionally characterised enzymes only use one substrate, synthesising one product. Mycoplasma pneumoniae, a common human pathogen with a small genome has only three proposed GTs. The bacterium was, however expected to have a greater number of GTs, due to its ability to make both glycolipids and capsule. Here we have determined the function of one of these enzymes, MPN483 and discovered its ability to both use different acceptors, and make elongated glycolipids with up to three galactose residues, with both DAG and ceramide as the base. Many of the synthesised glycolipids were also found to be immunogenic, hence showing their biological importance. The properties of lipids are known to be important for the function of a biological membrane. We have here shown that not only the charge but also the shape of the lipids are important for several protein mediated membrane processes in Echerichia coli, such as the function of the LacY.

Obesity is today a problem that has reached epidemic proportions. One of the causes of obesity is the over-consumption of energy. Fat is the most energy-dense nutrient, where the quality seems to be more important for the development of the metabolic diseases than the quantity. The fatty acid composition in serum lipid fractions can be used to mirror the dietary fat quality. Stearoyl-CoA-desaturase (SCD) is an enzyme that converts saturated to monounsaturated fatty acids. A surrogate measure of SCD activity can be estimated as a fatty acid ratio; 16:1/16:0 (palmitoleic acid/palmitic acid) and 18:1/18:0 (oleic acid/stearic acid). The aim of this project was to investigate the intra-day variation in the SCD-ratio in humans eating a standardized diet. The results showed that triacylglycerol and nonesterified fatty acid fractions in serum lipids had a significant variance in the 16:1/16:0 ratio during the day, whereas 18:1/18:0 ratio in the same fractions did not exhibit the same pattern. In this study 16:1/16:0 ratio also seems to be a better marker than 18:1/18:0 ratio for estimating SCD activity. For further evaluation of the intra-day variation there need to be a more long-term study of the SCD-activity for a larger group of subjects.

The continued increase in the demand for fossil fuels combined with their ever dwindling supply has prompted the search for a suitable alternative fuel. The research contained within this dissertation seeks to increase the lipid content of cellular feedstocks, improve extraction efficiencies of lipids, and understand the pathways involved in the production of fatty alcohols and triacylglycerides from microbial feedstocks. As part of this research the diatom, Cheatoceros gracilis, was grown at small and large scale to determine optimal growing conditions. No apparent nutrient stress trigger was required to initiate the accumulation of the biodiesel precursor triacylglyceride, unlike other documented algal strains. A follow-up to this project demonstrated that the microalga C. gracilis may utilize light intensity as a trigger for lipid production. A major difficulty in the production of biofuels from microorganisms is the expensive process of dewatering, drying, and extracting the lipid compounds from the cells. As part of this research, a process has been developed that allows for lipid extraction to occur in the presence of water at a point as low as 2 percent solids or 98 percent water. This process utilizes a single organic solvent that mixes well with microbial lipids, but poorly with water allowing for efficient extraction of lipids and fast solvent to water separation. This process greatly decreases the cost of the microbial biofuels production associated with the removal of water from cell slurries. Triacylglycerides and fatty alcohols are oleochemicals that are commonly used in industrial, pharmaceutical, and consumable processes. A predicted fatty acyl CoA reductase enzyme was cloned into an E. coli vector, expressed, characterized and shown to be active as a dual reductive enzyme reducing a fatty acyl CoA to its respective fatty alcohol, constituting the first enzyme of this type discovered in a bacterium. The process of triacylglyceride production in microbes is fairly well understood; however, the process that regulates this production has not yet been fully explored. As part of this research, the model yeast organism, Yarrowea lipolytica, is utilized to identify essential genes for citrate transport that if removed could result in increasing triacylglyceride production in vivo.

In the last few decades, an increasing number of physicists specialized in soft matter, including polymers, have turned their attention to biologically relevant materials. The properties of various molecules and fibres, such as DNA, RNA, proteins, and filaments of all sorts, are studied to better understand their behaviours and functions. Self-assembled biological membranes, or lipid bilayers, are also the focus of much attention as many life processes depend on these. Small lipid bilayers vesicles dubbed liposomes are also frequently used in the pharmaceutical and cosmetic industries. In this thesis, work is presented on both the elastic properties of polymers and the response of lipid bilayer vesicles to extrusion in narrow-channels. These two areas of research may seem disconnected but they both concern deformed soft materials. The thesis contains four articles: the first presenting a fundamental study of the entropic elasticity of circular chains; the second, a simple universal description of the effect of sequence on the elasticity of linear polymers such as DNA; the third, a model of the symmetric thermophoretic stretch of a nano-confined polymer; the fourth, a model that predicts the final sizes of vesicles obtained by pressure extrusion. These articles are preceded by an extensive introduction that covers all of the essential concepts and theories necessary to understand the work that has been done.

In vitro studies have shown that the major membrane phospholipid phosphatidylcholine (PC) can positively influence the incorporation of cholesterol in lipid membranes. The influence of PC on the cellular trafficking of LDL-derived free cholesterol was investigated. Sterol regulatory-defective (SRD)-4 cells are Chinese hamster ovary (CHO)-derived fibroblasts that display vastly elevated rates for the synthesis and catabolism of PC. SRD-4 cells harbor two known gene mutations: a mutation in the functional allele for SCAP, resulting in defective feedback suppression of cholesterol biosynthesis; and a loss-of-function mutation in the functional allele for acyl-CoA:cholesterol acyl transferase (ACAT), an endoplasmic reticulum (ER)-localized enzyme that esterifies free cholesterol. Incubation of SRD-4 cells with 50 µg/ml low density lipoprotein (LDL) for 18 h resulted in lysosomal accumulation of free cholesterol as revealed by filipin staining. This accumulation was not evident following LDL treatment of parental CHO7 cells, and was blunted in SRD-2 cells that express a constitutively-active form of SREBP-2 and overproduce cholesterol but have functional ACAT activity. Treatment of SRD-2 cells with LDL in the presence of an ACAT inhibitor 58-035 resulted in robust lysosomal cholesterol accumulation that was reversible upon drug washout, supporting that cholesterol trafficking in cholesterol-loaded cells is dependent on ACAT activity and, more specifically, ER free cholesterol levels. Lysosomal accumulation of LDL-derived cholesterol was prevented in SRD-4 cells supplemented with lyso-PC (50 µM), a substrate for PC synthesis through the reacylation pathway, and also in cells treated with bromoenol lactone (BEL), an inhibitor of phospholipase A2 implicated in bulk PC turnover. In a counter study, lysosomal LDL-derived cholesterol accumulation was induced in parental CHO-7 cells using R-propranolol, which inhibits the conversion of phosphatidic acid to diacylglycerol (DAG), a substrate in the CDP-choline pathway. This blockage was also relieved through co-treatment with lyso-PC. These studies support that PC to free cholesterol ratios in downstream organellar membranes can influence cholesterol trafficking out of lysosomal compartments in cholesterol-loaded cells.

Heat exposure causes several physiological and metabolic alterations. Although lipids are vital in sustaining energy production, heat-induced alterations in lipid metabolism have not been clearly established. CHAPTER 1 reviews the known metabolic alterations resulting from heat stress, with a specific focus on changes in whole-body lipid utilization and plasma lipids. CHAPTER 1also outlines the physiological changes caused by heat stress, and their role in reducing exercise performance. The study presented in CHAPTER 2 has shown that, compared to thermoneutral conditions, NEFA concentrations were 37% higher following passive heating and 34% higher following exercise in the heat, without significant changes in whole-body lipid utilization. In addition, the level of hyperthermia attained during passive pre-heating and exercise in the heat resulted in a 13% decrease in total external work and a significantly higher rate of perceived exertion. CHAPTER 3 summarizes the study results and presents the limitations and applications of the study.

Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.

The purpose of this research was to determine if a high cholesterol diet can affect tie rate of cholesterol synthesis or to cholesterol and fatty acid content of plasma membranes of mouse mammary a.denocarcinoma and normal mouse mammary gland tissue.Cholesterol synthesizing ability was determined by measuring the incorporation of 14C acetate into digitonin-precipitable sterols from both tumors and normal mammary tissue from Strong A Strain female mice fed a standard lab chow diet (control diet; or a 2% cholesterol experimental diet. Plasma membranes were isolated from both tenors and normal tissue by differential centrifugation. Cholesterol was measured spectrophotometrically. Fatty acids were extracted, methylated, and methylesters identified and quantified using gas liquid chromatography.The rate of incorporation of 111C acetate into digitonin-precipitated sterols in normal mammary tissue from mice fed the 2% cholesterol experimental diet was 1.5 times less than controls. Tumor tissue showed no significant difference. The fatty acid composition of tumor and normal mammary tissue plasma membranes from mice fed the 2% cholesterol experimental diet was similar to controls.There were higher percentages of C16:0 and C16.1 in normal plasma membranes of controls than mice fed the experimental diet. Cholesterol content of to or and normal mammary tissue plasma membranes from mice fed the experimental diet was similar to controls.It would appear that dietary cholesterol does have an effect on cholesterol synthesis in normal mammary tissue but not in marina y tumor tissue. Also dietary cholesterol does not have an effect on the fatty acid composition nor the cholesterol content in plasma membranes of mammary tumors or normal mammary tissue.Ball State UniversityMuncie, IN 47306

Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.

In the last few decades, an increasing number of physicists specialized in soft matter, including polymers, have turned their attention to biologically relevant materials. The properties of various molecules and fibres, such as DNA, RNA, proteins, and filaments of all sorts, are studied to better understand their behaviours and functions. Self-assembled biological membranes, or lipid bilayers, are also the focus of much attention as many life processes depend on these. Small lipid bilayers vesicles dubbed liposomes are also frequently used in the pharmaceutical and cosmetic industries. In this thesis, work is presented on both the elastic properties of polymers and the response of lipid bilayer vesicles to extrusion in narrow-channels. These two areas of research may seem disconnected but they both concern deformed soft materials. The thesis contains four articles: the first presenting a fundamental study of the entropic elasticity of circular chains; the second, a simple universal description of the effect of sequence on the elasticity of linear polymers such as DNA; the third, a model of the symmetric thermophoretic stretch of a nano-confined polymer; the fourth, a model that predicts the final sizes of vesicles obtained by pressure extrusion. These articles are preceded by an extensive introduction that covers all of the essential concepts and theories necessary to understand the work that has been done.