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.

The primary objective of this study was to quantify and characterise lipid deposition on soft (hydrogel) contact lenses, particularly those containing siloxane components. Studies involving a variety of <em>in vitro</em> doping and <em>in vivo</em> worn contact lenses were undertaken, in which lipid deposition was analyzed by either TLC or HPLC. Specific experiments were completed to optimize a method to extract the lipid from the lens materials, to compare the total lipid deposition on nine different hydrogel lenses and to analyze the effect that lipid deposition had on wettability. A method for extracting lipid from contact lenses using 2:1 chloroform: methanol was developed. This study also showed that siloxane-containing contact lens materials differ in the degree to which they deposit lipid, which is dependent upon their chemical composition. Small differences in lipid deposition that occur due to using variations in cleaning regimens were not identifiable through TLC, and required more sophisticated analysis using HPLC. Contact lens material wettability was found to be influenced by <em>in vitro</em> lipid deposition. Specifically, conventional hydrogels and plasma surface-treated silicone-hydrogel materials experienced enhanced wettability with lipid deposition. Reverse-phase HPLC techniques were able to quantify lipid deposits with increased sensitivity and accuracy. From the HPLC studies it was found that contact lens material, concentration of the lipid doping solution, and the composition of the lipid doping solution in <em>in vitro</em> deposition studies influenced the ultimate amount and composition of lipid deposits. <em>In vivo</em> HPLC studies showed that the final lipid deposition pattern was influenced by the interaction between the composition of the tear film and the various silicone hydrogel contact lens materials. In conclusion, HPLC analysis methods were more sensitive and quantitative than TLC. Lipid deposition was ultimately influenced by the concentration and composition of the lipid in the tear film and the contact lens material. Contact lens wettability was influenced by the presence and deposition of lipid onto the contact lens surfaces. Finally, this reverse-phase HPLC lipid analysis protocol was not the most sensitive, robust, or accurate. In the future, other methods of analysis should be explored.

Analytical instrumentation for quantitative in vivo stable isotope metabolic studies has included gas chromatography-mass spectrometry (GC-MS) and gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Limitations of existing MS techniques include excessive parent ion fragmentation, time-consuming sample preparation, and complex instrument operating parameters. In this thesis, procedures for set up and implementation of four GC-MS techniques are described. The first three replicate existing GC-MS single quadrupole methods on an ion trap, and are electron ionization (EI), external methane positive chemical ionization (PCI), and methane negative chemical ionization (NCI). The fourth method is a novel GC-MS mass-selected ion trap internal isobutane positive chemical ionization technique. Four groups of rats were administered isotopic linoleic acid, and liver tissue was collected for labelled linoleic and n-6 polyunsaturated fatty acids (PUFA) metabolites analyses. Qualitative utility of EI was confirmed, and its quantitative limitations exposed. Labelled 18:2n-6 and n-6 PUFA metabolites were detected using external methane PCI, though limited due to significant fragmentation. Methane NCI also detected labelled 18:2n-6, as well as minimizing fragmentation. However, time-consuming sample preparation and non-linear responses were major limitations. Internal isobutane PCI was useful in detecting isotopic 18:2n-6 and n-6 PUFA metabolites. Fragmentation was reduced compared to EI and external methane PCI. Limitations include fragmentation of HUFAs such as EPA and DHA. The novel internal isobutane PCI is more sensitive than external methane PCI and NCI, produces highly linear responses, is simpler and less expensive to operate than C-IRMS, offers reliable instrument operation, and sample preparation time is minimal. Regular quantitative analyses of HUFAs such as EPA and DHA may require further refinements such as using lower energy reagents than isobutane, including acetonitrile and ammonia.

ABSTRACT Background: Polyunsaturated fatty acids (PUFA) are found in nuts and seeds, salad dressings and vegetable oil and are prone to oxidation during storage and food preparation. Evidence supports that consumption of oxidized lipids promotes atherosclerosis and glucose intolerance in animal models. However there is a dearth of evidence with regard to the amount of oxidized lipids consumed and its association with parameters of adiposity and glucose homeostasis in humans. Objective: The objective of this study is to estimate the amount of oxidized lipids in common foods and the oxidized lipid consumption in the US population using the data from National Health and Nutrition Examination Survey (NHANES) 2005-06. The second objective of this study is to investigate if there is an association between consumption of oxidized lipids with markers of adiposity and glucose tolerance. Methods- Foods with possible high oxidized lipid content were selected from the NHANES food frequency questionnaire. Oxidized lipid content /Peroxide Values (PV) of these foods were determined from published values in the literature. Oxidized lipid consumption was stratified into tertiles to determine the relationship between consumption of oxidized lipids and markers of adiposity. Regression analysis was used to explore to the extent to which body fat % and HOMA- IR scores could be attributed to oxidized lipid intake. Results- The estimated mean daily consumption of oxidized lipids was 0.625 meq/kg of fat for the US population. Estimated mean consumption of oxidized lipids was significantly greater in men compared to women, in children compared to adults and among African Americans compared to other races. In both men and women it was observed that the markers of adiposity like body fat%, waist circumference, triceps skinfold decreased significantly with increased consumption of oxidized lipids. However in women (below 18 years) there was a significant increase in HOMA-IR with increased consumption of oxidized lipids. Conclusion- Increased consumption of oxidized lipids is associated with decreased fat mass but increased glucose intolerance in women, but not in men.

In this thesis we study the interactions of ions and cationic peptides with a negatively charged lipid bilayer in an ionic solution where the electrostatic interactions are screened. <br /><br /> We first examine the problem of charge renormalization and inversion of a highly charged bilayer with low dielectric constant. To be specific, we consider an asymmetrically charged lipid bilayer, in which only one layer is negatively charged. In particular, we study how dielectric discontinuities and charge correlations among lipid charges and condensed counterions influence the effective charge of the surface. When counterions are monovalent, e. g. , Na⁺, our mean-field approach implies that dielectric discontinuities can enhance counterion condensation. A simple scaling picture shows how the effects of dielectric discontinuities and surface-charge distributions are intertwined: Dielectric discontinuities diminish condensation if the backbone charge is uniformly smeared out while counterions are localized in space; they can, however, enhance condensation when the backbone charge is discrete. In the presence of asymmetric salts such as CaCl₂, we find that the correlation effect, treated at the Gaussian level, is more pronounced when the surface has a lower dielectric constant, inverting the sign of the charge at a smaller value of Ca²⁺ concentration. <br /><br /> In the last chapter we study binding of cationic peptides onto a lipid-bilayer membrane. The peptide not only interacts electrostatically with anionic lipids, rearranging their spatial distributions, but it can also insert hydrophobically into the membrane, expanding the area of its binding layer (i. e. , the outer layer). We examine how peptide charges and peptide insertion (thus area expansion) are intertwined. Our results show that, depending on the bilayer's surface charge density and peptide hydrophobicity, there is an optimal peptide charge yielding the maximum peptide penetration. Our results shed light on the physics behind the activity and selective toxicity of antimicrobial peptides, i. e. , they selectively rupture bacterial membranes while leaving host cells intact.

The primary objective of this study was to quantify and characterise lipid deposition on soft (hydrogel) contact lenses, particularly those containing siloxane components. Studies involving a variety of <em>in vitro</em> doping and <em>in vivo</em> worn contact lenses were undertaken, in which lipid deposition was analyzed by either TLC or HPLC. Specific experiments were completed to optimize a method to extract the lipid from the lens materials, to compare the total lipid deposition on nine different hydrogel lenses and to analyze the effect that lipid deposition had on wettability. A method for extracting lipid from contact lenses using 2:1 chloroform: methanol was developed. This study also showed that siloxane-containing contact lens materials differ in the degree to which they deposit lipid, which is dependent upon their chemical composition. Small differences in lipid deposition that occur due to using variations in cleaning regimens were not identifiable through TLC, and required more sophisticated analysis using HPLC. Contact lens material wettability was found to be influenced by <em>in vitro</em> lipid deposition. Specifically, conventional hydrogels and plasma surface-treated silicone-hydrogel materials experienced enhanced wettability with lipid deposition. Reverse-phase HPLC techniques were able to quantify lipid deposits with increased sensitivity and accuracy. From the HPLC studies it was found that contact lens material, concentration of the lipid doping solution, and the composition of the lipid doping solution in <em>in vitro</em> deposition studies influenced the ultimate amount and composition of lipid deposits. <em>In vivo</em> HPLC studies showed that the final lipid deposition pattern was influenced by the interaction between the composition of the tear film and the various silicone hydrogel contact lens materials. In conclusion, HPLC analysis methods were more sensitive and quantitative than TLC. Lipid deposition was ultimately influenced by the concentration and composition of the lipid in the tear film and the contact lens material. Contact lens wettability was influenced by the presence and deposition of lipid onto the contact lens surfaces. Finally, this reverse-phase HPLC lipid analysis protocol was not the most sensitive, robust, or accurate. In the future, other methods of analysis should be explored.

Analytical instrumentation for quantitative in vivo stable isotope metabolic studies has included gas chromatography-mass spectrometry (GC-MS) and gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Limitations of existing MS techniques include excessive parent ion fragmentation, time-consuming sample preparation, and complex instrument operating parameters. In this thesis, procedures for set up and implementation of four GC-MS techniques are described. The first three replicate existing GC-MS single quadrupole methods on an ion trap, and are electron ionization (EI), external methane positive chemical ionization (PCI), and methane negative chemical ionization (NCI). The fourth method is a novel GC-MS mass-selected ion trap internal isobutane positive chemical ionization technique. Four groups of rats were administered isotopic linoleic acid, and liver tissue was collected for labelled linoleic and n-6 polyunsaturated fatty acids (PUFA) metabolites analyses. Qualitative utility of EI was confirmed, and its quantitative limitations exposed. Labelled 18:2n-6 and n-6 PUFA metabolites were detected using external methane PCI, though limited due to significant fragmentation. Methane NCI also detected labelled 18:2n-6, as well as minimizing fragmentation. However, time-consuming sample preparation and non-linear responses were major limitations. Internal isobutane PCI was useful in detecting isotopic 18:2n-6 and n-6 PUFA metabolites. Fragmentation was reduced compared to EI and external methane PCI. Limitations include fragmentation of HUFAs such as EPA and DHA. The novel internal isobutane PCI is more sensitive than external methane PCI and NCI, produces highly linear responses, is simpler and less expensive to operate than C-IRMS, offers reliable instrument operation, and sample preparation time is minimal. Regular quantitative analyses of HUFAs such as EPA and DHA may require further refinements such as using lower energy reagents than isobutane, including acetonitrile and ammonia.

As a hydrophilic biopolymer, a DNA molecule is surrounded by water molecules in aqueous solution. The charge hopping mechanism indicates the competition between radical cation quenching by water molecules and migration along DNA partially determines the distance and efficiency of charge transport in DNA. Lipid can effectively bind DNA to induce hydrophobic environment around the DNA helix and reduce the water contact with bases in the DNA duplex. Therefore, the effect of water molecules on charge transport can be studied by comparison between nature DNA and DNA-lipid complexes. We synthesized several cationic lipids with various lengths of dialkyl chain (2, 8, 18) and spermine (Sp4+) binding core in this research, which posses strong DNA binding affinity due to their multi-charged spermine head-groups. Among those, C8GlySp4+ and C2GlySp4+ can form stable complex with DNA oligomer in aqueous solution, characterized by time dependent UV and CD spectrometry. C2GlySp4+ showed the similar inhibition on oxidative damage in GG steps as spermine while C8GlySp4+ demonstrated much more significant prohibitive effect at the same concentration. Since all the lipids bear the same binding core, they should afford the similar binding affinity towards DNA duplexes. we attributed the observation to the longer length of dialkyl group in C8GlySp4+, which can more effectively shield the DNA duplex from the water molecules than either spermine or C2GlySp4+. A kinetic model based on phonon-assist polaron hopping mechanism was proposed to rationalize the experimental results. The finding may give insight on the protection of DNA oxidative damage by reducing the access of the water molecule to DNA duplex and may have potential impact on the application of DNA as conducting biopolymer and protection of DNA in biological system.

To differentiate pyogenic brain abscess from other brain diseases such as necrotic glioblastomas is very important for clinic treatment. Cytosolic animo acids, lactate, alanine, succinate and acetate have been recognized as potential abscess markers. LCModel is a well-known tool to analyze the MRS data, as it provides opportunity of quantitative of metabolite concentration. Using MRS with LCModel to identify and quantitate these metabolites would benefit more precisely noninvasive diagnosis and treatment of pyogenic brain abscess. However, to differentiate the MR spectra of strongly overlapping metabolites are not easy. In this study, we validate the accuracy of LCModel on detecting these overlapping metabolites. We use some GAVA-simulated resonance spectra as our input signals and figure out the performance of LCModel analysis in different conditions. Our goal is to find an optimal analysis method to help the clinic diagnosis of abscess patients. Our result shows that the determination of basis sets is very important since the analyzed result might be different due to the improper selection of basis sets.

The effects of feeding with two high energy diets ( high carbohydrate and high lipid) and the feeding regime of the two diets on growth, feeding conversion rate, and body composition of the cobia were studied. Based on the observation of lipid redistribution under dietary regime change in rats, this study was aimed to understand how regime change affects the tissue lipid content in the cobia. The study had three parts: preliminary experiment, experiment I, and experiment II. The preliminary experiment was designed to find the proper time to switch the high energy diets and to see the adaptation of cobia to the highe energy dietary treatments. The experiment I was conducted to monitor the growth and body composition of cobia fed for thirty-two days with different experimental diets, including control diets, high carbohydrate diets (HC), high lipid diets (HL), and different feeding regimes (HC¡÷HL: feeding the HC diet for the first sixteen days and the HL diet for the subsequent sixteen days; HL¡÷HC: feeding the HL diet for the first sixteen days and the HC diet for the subsequent sixteen days. The experiment II was studied serum concentration of glucose, triacylglycerol, and free fatty acids and tissues triacylglycerol concentration in liver and white muscle. The fish fed with the HC diet had higher body weight and lower feeding conversion rate than the HL group in first sixteen days; however, the growth of the two groups was not significantly different during the thirty-two day period. The lipid content of dorsal muscle was significantly higher in HC¡÷HL than that in HL¡÷HC; wherease, the lipid content of ventral muscle and viscera was not signficantly affected. The concentrations of serum triacylglycerol, free fatty acid, and relative mean ratio of triacylglycerol in muscle to triacylglycerol in liver were significantly affected. The results of relative mean ratio of serum TG to serum FFA and relative mean ratio of muscle TG to liver TG, suggest that high carbohydrate diet drives de nova lipid production in liver, which circulates to the peripheral tissues for storage as triacylglycerol. High lipid diet preferentially offers energy for lipolysis to produce energy. These results are consistant with the results in rats. Our results show that high energy diets provided a higher growth rate than the control diet, but there were no growth difference in cobia fed high carbohydrate diets, or high lipid diets, or between different feeding regimes. The cobia fed the high carbohydrate diet and the high lipid diet might use different ways for lipid accumulation. These fed the high carbohydrate diet had formed more triacylglycerol than that these fed high lipid diets. The feeding regime shift between the high carbohydrate diet and the high lipid diet significantly affect the the lipid content of the dorsal muscle in the cobia.