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Using wavelets to analyze AFM images of thin films: Surface micelles and supported lipid bilayers

LANGMUIR 2004年第26期20卷 11557-11568页

作者： Carmichael, M Vidu, R Maksumov, A Palazoglu, A Stroeve, P Univ Calif Davis Dept Chem Engn & Mat Sci Davis CA 95616 USA

This paper presents micro- and nanoanalysis of thin films based on images obtained by atomic force microscopy (AFM). The analysis exploits the discrete wavelet transform and the resulting wavelet spectrum to study surface features. It is demonstrated that the wavelet technique can characterize micro- and nanosurface features and distinguish between similar surface structures. The use of a feature extraction method is shown. The method involves the separation of certain frequency content from the original AFM images and analyzing the data independently to gain quantitative information about the images. By using the feature extraction method, soft surfaces in water are analyzed and nanofeatures are measured. The packing of surface micelles of sodium dodecyl sulfate on a self-assembled monolayer is analyzed. The characteristics of pore formation, due to penetration of the antibacterial peptide protegrin, into a solid-supported lipid bilayer are quantified. The sizes of the pores are obtained, and it is observed that the line tension of the pores reduces the fluctuations of the lipid bilayer.

关键词： Antimicrobial Cationic Peptides image processing, computer-assisted Lipid Bilayers/chemistry Micelles Microscopy, Atomic Force Proteins/chemistry Sodium Dodecyl Sulfate/chemistry

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PROSPECTS FOR USING AN IVEM WITH A FEG FOR IMAGING MACROMOLECULES TOWARDS ATOMIC RESOLUTION

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ULTRAMICROSCOPY 1993年第1-4期49卷 407-416页

作者： ZHOU, ZH CHIU, W BAYLOR COLL MED W M KECK CTR COMPUTAT BIOL HOUSTON TX 77030 USA

Specimen preparation and imaging techniques for biological macromolecules have been improved to the point where attention to the electron-optical imaging conditions becomes a significant factor for achieving high resolution. A field emission gun (FEG) can provide an illumination source with a better spatial and temporal coherence suitable for imaging near atomic resolution. Our computational analysis of carbon film images taken between Scherzer focus and 1.1 mum underfocus (20X Scherzer focus) with the Hitachi 200 kV microscope with a cold field emission gun shows detectable contrast beyond 3.5 angstrom resolution. In biological imaging. a large defocus is often used to optimize the low-resolution contrast in order to facilitate the subsequent steps in computer reconstruction. An intermediate-voltage electron microscope (IVEM) would optimize the contrast at high resolution by reducing the temporal coherent effects. In theory, the IVEM would give a greater depth of field so that large macromolecular assemblies such as viruses and cellular structures can be interpreted and reconstructed reliably using the projection approximation. These experimental and theoretical considerations provide a rationale for designing a future IVEM with a FEG suitable for biological macromolecule imaging close to atomic resolution.

关键词： Fourier Analysis Fourier Analysis image processing, computer-assisted Microscopy, Electron/methods Specimen Handling Specimen Handling

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Direct observation of the release of phenylalanine from diphenylalanine nanotubes

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2006年第21期128卷 6903-6908页

作者： Sedman, Victoria L. Adler-Abramovich, Lihi Allen, Stephanie Gazit, Ehud Tendler, Saul J. B. Univ Nottingham Sch Pharm Lab Biophys & Surface Anal Nottingham NG7 2RD England Tel Aviv Univ George S Wise Fac Life Sci Dept Mol Microbiol & Biotechnol IL-69978 Tel Aviv Israel

fThe core recognition motif of the amyloidogenic beta-amyloid polypeptide is a dipeptide of phenylalanine. This dipeptide readily self-assembles to form discrete, hollow nanotubes with high persistence lengths. The simplicity of the nanotube formation, combined with ideal physical properties, make these nanotubes highly desirable for a range of applications in bionanotechnology. To fully realize the potential of such structures, it is first necessary to gain a comprehensive understanding of their chemical and physical properties. Previously, the thermal stability of these nanotubes has been investigated by electron microscopy. Here, we further our understanding of the structural stability of the nanotubes upon dry-heating using the atomic force microscope (AFM), and for the first time identify their degradation product utilizing time-of flight secondary-ion mass spectrometry. We show that the nanotubes are stable at temperatures up to 100 degrees C, but on heating to higher temperatures begin to lose their structural integrity with an apparent collapse in tubular structure. With further increases in temperature up to and above 150 degrees C, there is a degradation of the structure of the nanotubes through the release of phenylalanine building blocks. The breakdown of structure is observed in samples that are either imaged at elevated temperatures or imaged following cooling, suggesting that once phenylalanine is lost from the nanotubes they are susceptible to mechanical deformation by the imaging AFM probe. This temperature-induced plasticity may provide novel properties for these peptide nanotubes, including possible applications as scaffolds and drug delivery devices.

关键词： Hot Temperature image processing, computer-assisted Microscopy, Atomic Force Nanotubes/chemistry Phenylalanine/analogs & derivatives Phenylalanine/chemistry Spectrometry, Mass, Secondary Ion/methods

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Synthesis and utilization of monodisperse hollow polymeric particles in photonic crystals

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2004年第25期126卷 7940-7945页

作者： Xu, XL Asher, SA Univ Pittsburgh Dept Chem Pittsburgh PA 15260 USA

We developed a process to fabricate 150-700 nm monodisperse polymer particles with 100500 nm hollow cores. These hollow particles were fabricated via dispersion polymerization to synthesize a polymer shell around monodisperse SiO2 particles. The SiO2 cores were then removed by HF etching to produce monodisperse hollow polymeric particle shells. The hollow core size and the polymer shell thickness, can be easily varied over significant size ranges. These hollow polymeric particles are sufficiently monodisperse that upon centrifugation from ethanol they form well-ordered close-packed colloidal crystals that diffract light. After the surfaces are functionalized with sulfonates, these particles self-assemble into crystalline colloidal arrays in deionized water. This synthetic method can also be used to create monodisperse particles with complex and unusual morphologies. For example, we synthesized hollow particles containing two concentric-independent, spherical polymer shells, and hollow silica particles which contain a central spherical silica core. In addition, these hollow spheres can be used as template microreactors. For example, we were able to fabricate monodisperse polymer spheres containing high concentrations of magnetic nanospheres formed by direct precipitation within the hollow cores.

关键词： Alkanesulfonates/chemistry Biocompatible Materials/chemical synthesis Colloids/chemistry Crystallization image processing, computer-assisted Light Light Microscopy, Electron/methods Nanotechnology Particle Size Photons Photons Polymers/chemical synthesis Silicon Dioxide/chemistry

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Structural analysis of the photosystem I supercomplex of cyanobacteria induced by iron deficiency

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BIOCHEMISTRY 2003年第11期42卷 3180-3188页

作者： Nield, J Morris, EP Bibby, TS Barber, J Univ London Imperial Coll Sci Technol & Med Dept Biol Sci Wolfson Labs London SW7 2AZ England

Here we describe the three-dimensional structure of the newly discovered CP43'-photosystem I (PSI) supercomplex of cyanobacteria calculated by single-particle analysis of images obtained by electron cryomicroscopy (cryo-EM). This large membrane protein complex has a molecular mass of approximately 2 MDa and is found in cyanobacteria when grown in iron deficient media. It is composed of a reaction center trimer surrounded by 18 subunits of the chlorophyll a binding CP43'protein, encoded by the isiA gene, which increases the light harvesting capacity of PSI by similar to70%. By modeling higher-resolution structural data obtained from X-ray crystallography into the three-dimensional (3D) cryo-EM map, we have been able to gain a better understanding of the structure and functional properties of this supermolecular complex. We have identified three separate clusters of chlorophyll molecules at the periphery of the PSI core which may aid energy transfer from the CP43' antenna ring to the reaction center. Moreover, it is shown that despite the replacement of ferredoxin with flavodoxin as an electron acceptor under iron stress conditions, the 3D map has density to accommodate the extrinsic proteins, PsaC, PsaD, and PsaE. The presence of these three proteins was also confirmed by immunoblotting.

关键词： Cryoelectron Microscopy Crystallography, X-Ray Cyanobacteria/chemistry image processing, computer-assisted Iron/chemistry Models, Molecular Photosynthetic Reaction Center Complex Proteins/chemistry Photosynthetic Reaction Center Complex Proteins/chemistry Photosynthetic Reaction Center Complex Proteins/ultrastructure Photosynthetic Reaction Center Complex Proteins/ultrastructure Protein Conformation

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Programmable fluidic production of microparticles with configurable anisotropy

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2008年第4期130卷 1335-1340页

作者： Sung, Kyung Eun Vanapalli, Siva A. Mukhija, Deshpremy Mckay, Hugh A. Millunchick, Joanna Mirecki Burns, Mark A. Solomon, Michael J. Univ Michigan Dept Chem Engn Ann Arbor MI 48109 USA Univ Michigan Dept Mat Sci & Engn Ann Arbor MI 48109 USA Univ Michigan Dept Biomed Engn Ann Arbor MI 48109 USA

We report a technique for continuous production of microparticles of variable size with new forms of anisotropy including alternating bond angles, configurable patchiness, and uniform roughness. The sequence and shape of the anisotropic particles are configured by exploiting a combination of confinement effects and microfluiclics to pack precursor colloids with different properties into a narrow, terminal channel. The width and length of the channel relative to the particle size fully specify the configuration of the anisotropic particle that will be produced. The precursor spheres packed in the production zone are then permanently bonded into particles by thermal fusing. The flow in the production zone is reversed to release the particles for collection and use. Particles produced have linear chain structure with precisely configured, repeatable bond angles. With software programmable microfluidics, sequence and shape anisotropy are combined to yield synthesized homogeneous (type "A"), surfactantlike (type "A-B") or triblock (type "A-B-A") internal sequences in a single device. By controlling the dimensions of the microfluidic production zone, triangular prisms and particles with controlled roughness and patchiness are produced. The fabrication method is performed with precursors spheres with diameter as small as 3.0 mu m.

关键词： Anisotropy Drug Carriers Drug Delivery Systems Electrochemistry/methods image processing, computer-assisted Microchemistry/methods Microfluidic Analytical Techniques Microfluidics Microspheres Models, Chemical Nanotechnology/methods Particle Size Polystyrenes/chemistry Software Temperature

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Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography

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ULTRAMICROSCOPY 2006年第3期106卷 240-254页

作者： Winkler, H Taylor, KA Florida State Univ Inst Mol Biophys Tallahassee FL 32306 USA

An image alignment method for electron tomography is presented which is based on cross-correlation techniques and which includes a simultaneous refinement of the tilt geometry. A coarsely aligned tilt series is iteratively refined with a procedure consisting of two steps for each cycle: area matching and subsequent geometry correction. The first step, area matching, brings into register equivalent specimen regions in all images of the tilt series. It determines four parameters of a linear two-dimensional transformation, not just translation and rotation as is done during the preceding coarse alignment with conventional methods. The refinement procedure also differs from earlier methods in that the alignment references are now computed from already aligned images by reprojection of a backprojected volume. The second step, geometry correction, refines the initially inaccurate estimates of the geometrical parameters, including the direction of the tilt axis, a tilt angle offset, and the inclination of the specimen with respect to the support film or specimen holder. The correction values serve as an indicator for the progress of the refinement. For each new iteration, the correction values are used to compute an updated set of geometry parameters by a least squares fit. Model calculations show that it is essential to refine the geometrical parameters as well as the accurate alignment of the images to obtain a faithful map of the original structure. (c) 2005 Elsevier B.V. All rights reserved.

关键词： Animals Fourier Analysis Fourier Analysis image processing, computer-assisted Microscopy, Electron/methods Microscopy, Electron/statistics & numerical data Proteins/ultrastructure Software Software Design Tomography/methods Tomography/statistics & numerical data

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Making a Tool of an Artifact: The Application of Photoinduced Lo Domains in Giant Unilamellar Vesicles to the Study of Lo/Ld Phase Spinodal Decomposition and Its Modulation by the Ganglioside GM1

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LANGMUIR 2011年第24期27卷 15074-15082页

作者： Staneva, Galya Seigneuret, Michel Conjeaud, Helene Puff', Nicolas Angeova, Miglena I. Univ Paris Diderot UMR 7057 Paris France CNRS Paris France Bulgarian Acad Sci Inst Biophys & Biomed Engn Sofia Bulgaria Univ Paris 06 UPMC Dept Phys UFR 925 Paris France

Electroformed giant unilamellar vesicles containing liquid-ordered Lo domains are important tools for the modeling of the physicochemical properties and biological functions of lipid rafts. Lo domains are usually imaged using fluorescence microscopy of differentially phase-partionioning membrane-embedded probes. Recently, it has been shown that these probes also have a photosensitizing effect that leads to lipid chemical modification during the fluorescence microscopy experiments. Moreover, the lipid reaction products are able as such to promote Lo microdomain formation, leading to potential artifacts. We show here that this photoinduced effect can also purposely be used as a new approach to study Lo microdomain formation in giant unilamellar vesicles. Photosensitized lipid modification can promote Lo microdomain appearance and growth uniformly and on a faster time scale, thereby yielding new information on such processes. For instance, in egg phosphatidylcholine/egg sphingomyelin/cholesterol 50:30:20 (mol/mol) giant unilamellar vesicles, photoinduced Lo microdomain formation appears to occur by the rarely observed spinodal decomposition process rather than by the common nucleation process usually observed for Lo domain formation in bilayers. Moreover, temperature and the presence of the ganglioside GM1 have a profound effect on the morphological outcome of the photoinduced phase separation, eventually leading to features such as bicontinuous phases, phase percolation inversions, and patterns evoking double phase separations. GM1 also has the effect of destabilizing Lo microdomains. These properties may have consequences for Lo nanodomains stability and therefore for raft dynamics in biomembranes. Our data show that photoinduced Lo microdomains can be used to obtain new data on fast raft-mimicking processes in giant unilamellar vesicles.

关键词： Animals Artifacts Biomimetics/methods Chickens Cholesterol/chemistry Cholesterol/metabolism G(M1) Ganglioside/chemistry G(M1) Ganglioside/pharmacology image processing, computer-assisted Kinetics Light Light Lipid Bilayers/chemistry Lipid Bilayers/metabolism Membrane Microdomains/chemistry Membrane Microdomains/drug effects Membrane Microdomains/metabolism Membrane Microdomains/radiation effects Microscopy, Fluorescence Microscopy, Video Phosphatidylcholines/chemistry Phosphatidylcholines/metabolism Photochemical Processes/radiation effects Sphingomyelins/chemistry Sphingomyelins/metabolism Temperature Time Factors Unilamellar Liposomes/chemistry Unilamellar Liposomes/metabolism

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SEPARATION AND CHARACTERIZATION OF RICE PROTEINS

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ELECTROPHORESIS 1994年第5期15卷 708-720页

作者： TSUGITA, A KAWAKAMI, T UCHIYAMA, Y KAMO, M MIYATAKE, N NOZU, Y SCI UNIV TOKYO DEPT APPL BIOL SCI NODA CHIBA JAPAN SCI UNIV TOKYO FAC PHARMACEUT SCI SHINJUKU KU TOKYO JAPAN NATL INST AGROBIOL RESOURCES TSUKUBA IBARAKI JAPAN

Rice proteins from nine tissues and one organelle (leaf, chloroplast, stem, root, germ, dark germinated seedling, seed, bran, chaff and callus) were isolated and then separated by two-dimensional gel electrophoresis (2-DE). The protein spots were characterized according to molecular weight, isoelectric point and partial amino-terminal sequence. Electrophoresis was carried out by isoelectric focusing (IEF), nonequilibrium pH gradient electrophoresis (NEPHGE) and immobilized pH gradient (IPG) in the first dimension, and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension. With the aid of nine marker proteins, the patterns of IEF, NEPHGE and IPG 2-DE gels were graphically combined by computer into a single synthetic image for each tissue, respectively, and these images for the nine tissues and one organelle were again combined into a single 2-DE image for the integrated rice protein spots. The rice 2-DE gel image resolved 4892 proteins. About 3% of the spots are characterized by amino-terminal sequencing.

关键词： Amino Acid Sequence Databases, Factual Electrophoresis, Gel, Two-Dimensional image processing, computer-assisted Molecular Sequence Data Oryza sativa/chemistry Oryza sativa/chemistry Plant Proteins/isolation & purification Reference Standards

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Two-color green fluorescent protein time-lapse imaging

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BIOTECHNIQUES 1998年第5期25卷 838-+页

作者： Ellenberg, J Lippincott-Schwartz, J Presley, JF NICHHD NIH Cell Biol & Metab Branch Bethesda MD 20892 USA

The Aequorea victoria green fluorescent protein (GFP) is widely recognized as a powerful tool in cell biology, serving as a vital reporter for monitoring localization and dynamics of intracellular proteins and organelles over time. GFP variants with shifted spectral characteristics have been described and offer enormous potential Sor double-labeling experiments and protein-protein interaction studies. However, most GFP variant combinations are not suitable for double-label, time-lapse imaging experiments because of either extremely rapid photobleaching of blue-shifted GFP variants or crossover of their excitation and emission spectra, which must then be computer corrected. Here, we describe the successful use of two photostable spectral GFP variants, W7 and 10C, in dual-color, time-lapse imaging of fusion proteins in living cells using either wide-field or confocal microscopy. W7 and 10C were highly photostable during repetitive long-term imaging and were cleanly separated by their different excitation spectra alone with negligible crossover of fluorescence. We present time-lapse image sequences of COS-7 cells co-expressing both a marker of the Golgi complex (galactosyl transferase) fused to W7 and a marker of the nuclear envelope (lamin-B receptor) fused to 10C. To our knowledge, these image sequences provide the first simultaneous visualization of Golgi and nuclear envelope membranes in living cells.

关键词： Animals Color Perception COS Cells Galactosyltransferases/genetics Golgi Apparatus/metabolism Green Fluorescent Proteins image processing, computer-assisted Luminescent Proteins/genetics Luminescent Proteins/metabolism Microscopy, Confocal Microscopy, Video Nuclear Envelope/metabolism Receptors, Cytoplasmic and Nuclear/genetics Recombinant Fusion Proteins/genetics Recombinant Fusion Proteins/metabolism Spectrometry, Fluorescence

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