Lipid visualization

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read several different structural file formats and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. 

Barza, M., Stuart, M., and Szoka, F. (1987). Effect of size and lipid composition on the pharmacokinetics of intravitreal liposomes, Invest. Ophthalmol. Visual Sci., 28, 893-900. 

Direct observation of molecular diffusion is the most powerful approach to evaluate the bilayer fluidity and molecular diffusivity. Recent advances in optics and CCD devices enable us to detect and track the diffusive motion of a single molecule with an optical microscope. Usually, a fluorescent dye, gold nanoparticle, or fluorescent microsphere is used to label the target molecule in order to visualize it in the microscope [31-33]. By tracking the diffusive motion of the labeled-molecule in an artificial lipid bilayer, random Brownian motion was clearly observed (Figure 13.3) [31]. As already mentioned, the artificial lipid bilayer can be treated as a two-dimensional fluid. Thus, an analysis for a two-dimensional random walk can be applied. Each trajectory observed on the microscope is then numerically analyzed by a simple relationship between the displacement, r, and time interval, T,... 

Figure 13.6 (a) Confocal micrograph of a circularly self-spreading lipid monolayer. A rhodamine-labeled lipid is doped to visualize the spreading behavior, (b) A schematic illustration of the front edge of the self-spreading lipid monolayer [51]. 

The reagent used for the deteetion may be speeifie to a special functional group or specific lipids or may be a nonspecific reagent that makes all hpids visible. The most commonly used reagent that is nonspecific for any lipid group is 0.1% (w/v) 2, 7 -dichlorofuorescein in 95% methanol. This is mainly useful when the plates have been developed in acidic solvents. The lipid spots or bands can be visualized as yellow spots or bands under UV light. After the plates are developed in alkaline solvents, an aqueous solution of Rhodamine 6G (0.01%) can be used, and lipid spots can be seen as pink spots under UV. Because both these methods are nondestructive, they can be effectively used in PTLC so that the separated sample bands can be scraped off and used for further analysis. 

Advantages Simplified regimen for patient Increased patient compliance at home Decreased labor Decreased costs Decreased risk of contamination (due to less manipulation) Minimize infusion-related reactions from intravenous lipid emulsions Decreased vein irritation (especially with PPN) Improved stability compared to TNA Increased number of compatible medications Decreased bacterial growth compared to TNA Easier visual inspection Can use 0.22-micron bacterial retention filter Cost savings if unused (i.e. not spiked) intravenous lipid emulsion can be reused... 

Disadvantages Decreased stability compared to 2-in-1 PN Cannot use 0.22-micron bacterial retention filter Increased bacterial growth compared to 2-in-1 PN Visual inspection is difficult Limited compatibility with medications Increased labor and costs (if intravenous lipid emulsion infused separately) Increased vein irritation, especially if PPN is not coinfused with intravenous lipid emulsion... 

Components of the tear attach to contact lenses by electrostatic and van der Waals forces and build up to form deposits. Deposits on the surface and in the lens matrix may result in reduced visual acuity, irritation, and in some instances serious ocular complications. The composition of deposits vary because of the complexity of an individual s ocular physiology-pathology. Lysozyme is a major component of soft lens deposits, especially found on high-water-content ionic lenses [312]. Calcium [313] and lipids [314] are infrequent components of deposits, occurring as inorganic salts, organic salts, or as an element of mixed deposits, or as a combination thereof [315,316]. 

The visual pigment present in rods has been termed rhodopsin and consists of 11-m-retinal, a derivative of vitamin A1( and a lipoprotein called opsin. Recent evidence(43) suggests that in native rhodopsin the retinal chromo-phore is covalently bonded to a phosphatidylethanolamine residue of the lipid portion of opsin. The structure of 1 l-cis-retinal is as follows ... 

FIGU RE 10.13 Schematic drawing of the distribution of xanthophyll molecules between raft domain (DRM) and bulk domain (DSM) in lipid bilayer membranes. For this illustration, the xanthophyll partition coefficient between domains is the same as obtained experimentally for raft-forming mixture. However, to better visualize the observed effect in the drawing, the number of lipid molecules was decreased and the total number of xanthophyll molecules was increased about 10 times. (From Wisniewska, A. and Subczynski, W.K., Free Radio. Biol. Med., 40, 1820, 2006. With permission.)... 

Hennesthal, C., Steinem, C., Pore-spanning lipid bilayers visualized by scanning force microscopy, J. Am. Chem. Soc. 2000, 122, 8085-8086. 

Fig. 6.20. Types of assays to visualize lipid trafficking in membranes. (A) Self-quenching method. Here the self-quenching is released upon transfer to unlabeled acceptor membranes that are usually in large excess. (B) FRET assays. Here the donor membrane contains a transferable lipid (green) that is quenched by FRET to a non transferable acceptor lipid (red). Upon transfer to an unlabeled acceptor membrane the green-labeled lipid becomes unquenched. 

IMS is a new, developing technique to visualize biomolecule maps in tissue. IMS has opened a new frontier in medicine as well as in clinical applications. Lipids and low-molecular-weight compounds in tissue sections cannot be observed with conventional microscopic or electron microscopic techniques therefore, no distribution map of these molecules in a tissue structure has been described in the scientific literature or in medical textbooks. However, IMS is bringing to light the characteristic distribution map of lipids (Fig. 21.11) this map made a major impact to lipid research. 

The structure and roles of membrane microdomains (rafts) in cell membranes are under intensive study but many aspects are still unresolved. Unlike in synthetic bilayers (Fig. 2-2), no way has been found to directly visualize rafts in biomembranes [22]. Many investigators operationally define raft components as those membrane lipids and proteins (a) that remain insoluble after extraction with cold 1% Triton X-100 detergent, (b) that are recovered as a low density band that can be isolated by flotation centrifugation and (c) whose presence in this fraction should be reduced by cholesterol depletion. 

Information concerning myelin structure is also available from electron microscope studies, which visualize myelin as a series of alternating dark and less dark lines (protein layers) separated by unstained zones (the lipid hydrocarbon chains) (Figs 4-4 to 4-7). There is asymmetry in the staining of the protein layers. The less dark, or intraperiod, line represents the closely apposed outer protein... 

Immunocytochemical methods have been widely applied to visualize proteins, carbohydrates, or lipids in sectioned material. The advantage of using immunocytochemistry is to be able to localize the molecules of interest within the tissue. Several procedures have been described. Basically, these procedures can be split into four main steps that are described in subheadings (1) tissue preparation, (2) the primary antibodies, (3) the visualization of the target, and (4) enhancement of signals with antibody complexes. In addition, a protocol for alkaline phosphatase will be presented in detail in Subheading 5. The terms primary and secondary antibodies refer to the order in which they are applied to the target. The immunocytochemical procedures are not limited to sectioned... 

Benchimol M, De Souza W. Tritrichomonas foetus, cytochemical visualization of the endoplasmic reticulum-Golgi complex and lipids. Exper Parasitol 1985 59 51-58. 

Living cells visualization of membranes, lipids, proteins, DNA, RNA, surface antigens, surface glycoconjugates membrane dynamics membrane permeability membrane potential intracellular pH cytoplasmic calcium, sodium, chloride, proton concentration redox state enzyme activities cell-cell and cell-virus interactions membrane fusion endocytosis viability, cell cycle cytotoxic activity... 

Lipids may be visualized on thin-layer plates using a general stain but this does not usually indicate the nature of the lipid present. Many of these are destructive (Table 12.10) and the lipid cannot be analysed further after elution from the plate, but other stains are non-destructive (Table 12.11). There... 

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