Life Sciences Commons^™

The Chromatin Structure Of Well-Spread Demembranated Human Sperm Nuclei Revealed By Atomic Force Microscopy, M. J. Allen, E. M. Bradbury, R. Balhorn

Scanning Microscopy

The fundamental structure formed when genomic DNA is packaged by protamine in the human sperm nucleus still remains essentially unresolved. It is known that the binding of protamine, a small arginine-rich protein, to DNA generates a large dense, hydrophobic complex making the sperm chromatin structure difficult to study microscopically. To visualize the internal nuclear structures, isolated human sperm nuclei were swollen extensively in saline buffer using only a reducing agent. The nuclei were swollen during deposition onto coverglass and then imaged in the atomic force microscope (AFM). The two main results obtained from imaging individual well-spread nuclei indicate that native …

Atomic Force Microscopy Of Humic Acids, A. Ikai, R. Osterberg

Scanning Microscopy

Atomic force microscopic (AFM) images of humic acids show discrete, globular particles, where particles of the order of magnitude 100 to 300 nm dominate the image fields; the humic acids had been grown to a steady state at pH 5.0. The AFM data are consistent with our previously reported small-angle neutron scattering (SANS) study done under similar conditions. In further agreement, the cluster-cluster interactions shown in our previous SANS study may have their counterparts in closely interacting particles appearing as twin particles in the AFM images.

Imaging The Electrocyte Of Torpedo Marmorata By Scanning Force Microscopy, L. I. Pietrasanta, A. Schaper, G. Q. Fox, F. J. Barrantes, T. M. Jovin

Scanning Microscopy

Scanning force microscopy (SFM) and scanning electron microscopy (SEM) were used to examine the tissue structure of the electric organ of Torpedo marmorata in air and in liquid after applying fracturing and cryosectioning techniques and chemical fixation. The electric organ is organized in columns of stacked electrocytes, arranged in a honeycomb pattern. The columns were cut along a plane normal to the cell stack and thin sections were transferred to polylysine coated glass coverslips. The polarity of the electrocytes was made apparent by immunofluorescence microscopy directed to different domains of the acetylcholine receptor (AChR), thus revealing the innervated face of …

Deposition Of Supercoiled Dna On Mica For Scanning Force Microscopy Imaging, B. Samori, I. Muzzalupo, G. Zuccheri

Scanning Microscopy

The deposition of DNA molecules on mica is driven and controlled by the ionic densities around DNA and close to the surface of the substrate. Dramatic improvements in the efficiency and reproducibility of DNA depositions were due to the introduction of divalent cations in the deposition solutions. The ionic distributions on DNA and on mica determine the mobility of adsorbed DNA molecules, thus letting them assume thermodynamically equilibrated conformations, or alternatively trapping them in non-equilibrated conformations upon adsorption.

With these prerequisites, mica does not seem like an inert substrate for DNA deposition for microscopy, and its properties greatly affect the …

Fluorescence Imaging And Spectroscopy Of Biomaterials In Air And Liquid By Scanning Near-Field Optical/Atomic Force Microscopy, H. Muramatsu, N. Chiba, K. Nakajima, T. Ataka, M. Fujihira, J. Hitomi, T. Ushiki

Scanning Microscopy

We have developed scanning near-field optical/atomic force microscopy (SNOM/AFM). The SNOM/AFM uses a bent optical fiber simultaneously as a dynamic force AFM cantilever and a SNOM probe. Resonant frequency of the optical fiber cantilever is 15-40 kHz. Optical resolution of the SNOM/AFM images shows less than 50 nm. The SNOM/ AFM system contains photon counting system and polychrometer/intensified coupled charge devise (ICCD) system to observe fluorescence image and spectrograph of micro areas, respectively. Cultured cells were stained with fluorescein isothiocyanate (FITC)-labeled anti-keratin antibody or FITC-labeled phalloidin after treatment with Triton X-100. Fluorescence and topographic images were obtained in air and …

Towards In Situ Atomic Force Microscopy Imaging Of Biofilm Growth On Stainless Steel, D. T. Goddard, A. Steele, I. B. Beech

Scanning Microscopy

Atomic force microscopy (AFM) has been used to visualise the formation of bacterial biofilms on polished surfaces of 316 stainless steel. Imaging under ambient conditions revealed both the bacterial cells and the matrix of exopolymeric substances (EPS). These images exhibited good resolution with cell surface features as small as 30 nm distinguishable. In situ imaging was also carried out, and although the resolution was considerably reduced, images revealing the process of bacteria division have been obtained.

Atomic Force Microscopy Investigation Of Radiation-Induced Dna Double Strand Breaks, D. Pang, G. Popescu, J. Rodgers, B. L. Berman, A. Dritschilo

Scanning Microscopy

We have used atomic force microscopy (AFM) to study radiation-induced DNA double strand breaks. Double-stranded plasmid DNA was irradiated with 18-MeV electrons in aqueous buffer, using a medical linear accelerator. Doses of 50, 100, 150, and 200 Gy were delivered to DNA samples, and atomic force microscopy was used to measure the length of each DNA fragment. From these measurements, we obtained the average length of the irradiated DNA for each sample and found a linear-quadratic relationship between the average length and radiation dose.

Contact Force Dependence On Relative Humidity: Investigations Using Atomic Force Microscopy, E. Finot, E. Lesniewska, J. -C. Mutin, S. I. Hosain, J. -P. Goudonnet

Scanning Microscopy

This paper deals with the ability of scanning force microscopy to determine contact forces of various materials. Indeed, with high spring constants at low relative humidity, the nature of the material can be determined by measurement of the contact force as the tip approaches. Cantilevers with a high spring constant are used to achieve solid-solid contact for the tip-sample system. The capillary force estimation provides information on the development of the height of the water meniscus formed between the tip and different surfaces depending on the relative humidity. Finally, we focus our attention on measurements of moduli of elasticity which …

Volume Determination Of Human Metaphase Chromosomes By Scanning Force Microscopy, Wolfgang Fritzsche, Eric Henderson

Scanning Microscopy

The scanning force microscope (SFM) yields the topography of the investigated surface. A procedure was developed which starts from this three-dimensional information to estimate the volume of a biological specimen. The volume of spread human metaphase chromosomes was determined in air and rehydrated in aqueous buffer. A difference of the determined volume of a air-dried metaphase chromosome set was found compared to values from electron microscopic investigations, and could be correlated with differences in the hydration state of the chromosomes. SFM-based relative volumes of air-dried chromosomes resembles literature data regarding volume range and distribution. Possible application of SFM-based relative volume …

Atomic Force Microscopy Study Of Fine Structures Of The Entire Surface Of Red Blood Cells, P. -C. Zhang, C. Bai, Y. -M. Huang, H. Zhao, Y. Fang, N. -X. Wang, Q. Li

Scanning Microscopy

Glutaraldehyde-fixed red blood cells were imaged by tapping mode atomic force microscopy (TMAFM) in air at room temperature. The results show that TMAFM can visualize the morphology of the red blood cell at both cellular and nanometer scales. The scan size covers the range from several hundred nanometers to more than one hundred micrometers. TMAFM not only has a higher resolution than the optical microscope, but also can observe biological samples without precoating as required for scanning electron microscopy (SEM). The AFM images of the entire surface of an uncoated red blood cell with nanometer resolution are successfully reconstructed by …

Atomic Force Microscopy Of Neuron Networks, A. Cricenti, G. De Stasio, R. Generosi, P. Perfetti, M. T. Ciotti, D. Mercanti

Scanning Microscopy

We imaged uncoated neuron networks by an atomic force microscope in the repulsive regime of contact mode. Images of granule cells and their axons have been clearly revealed with details smaller than 20 nm. The good stability of the sample and the mechanical reproducibility of the microscope allowed the imaging of a neuron culture area of several square microns. By combining tens of images, we were able to reconstruct a highly defined neuronal network. Furthermore, the images were very reproducible over repeated scanning acquisition, demonstrating the mechanical and thermal stability of the instrument-sample system.

Tip-Induced Modifications In Scanning Tunneling Microscopy And Atomic Force Microscopy, K. Cho, J. D. Joannopoulos

Scanning Microscopy

Tip-induced modifications of microscopic processes in scanning tunneling microscopy (STM) and atomic force microscopy (AFM) of the Si(l00) surface are investigated with ab initio total energy pseudopotential calculations. The results of the calculations lead to a new understanding of the microscopic STM measurement process and the micro-mechanical changes (hysteresis and plastic deformation) in the AFM process. In particular, in the latter case, the results predict that the tip can be used to flip dimers on the surface, from one buckled configuration to the other, reversibly, and without inducing damage to either the intrinsic surface or the tip.

Scanning Force Microscopy Of Chromatin, Wolfgang Fritzsche, James Vesenka, Eric Henderson

Scanning Microscopy

Scanning force microscopy (SFM) is a new method to obtain the topography of surfaces with nanometer-resolution. The ability to image under liquids makes the technique attractive for biological applications, especially for the determination of the ultrastructure of biomolecules under native conditions. One growing field of interest is the investigation of chromatin and chromatin-related structures. Different levels of chromatin condensation were the subject of several previous SFM investigations, from the nucleosomal chain, to the 30-nm fiber, ending with the metaphase chromosome. The SFM yielded new information on such fundamental problems as the core spacing of the nucleosomal chain, the internal structure …

Optical Microscopy And Atomic Force Microscopy Imaging Of 2,4,6-Trinitrotoluene Droplets And Clusters On Mica, D. O. Henderson, M. A. George, A. Burger, R. Mu, Zhiyu Hu, G. C. Huston

Scanning Microscopy

Optical and atomic force microscopy (AFM) were used to image 2,4,6-trinitrotoluene (TNT) on a cleaved mica (001) surface. The vapor deposition of TNT resulted in ellipsoidal drop formation on the mica surface. The growth rate of the drop diameter was found to be linear with vapor dosing time while the drop density followed a 1/r² dependence, where r is the length of the major axis of the ellipsoid, for increasing dosing times. TNT platelets surrounded by a region depleted of drops were observed after 8 hours of dosing. The depleted region is attributed to a 10% shrinkage for liquid-solid …

Can Photo- And Cathodoluminescence Be Regarded As Complementary Techniques?, S. Myhajlenko, R. A. Puechner, J. L. Edwards, D. B. Davito

Scanning Microscopy

Photoluminescence (PL) usually provides macroscopic, high quality spectroscopic data. Cathodoluminescence (CL), on the other hand, offers the same information with microscopic imaging. However, replicating PL signatures in a CL system is not straightforward since matching experimental conditions, such as temperature and excitation density, is difficult. The matter is further exacerbated by inherent differences in the nature of excitation: electrons versus photons. Our work with high purity semiconductors suggests that CL is generally more sensitive to excitation "circumstance" than PL. For example, electrons can cause sample charging and contamination-related phenomena that dramatically affect CL. Changes in surface attributes (e.g., by chemical …

Atomic Step Organization In Homoepitaxial Growth On Gaas(111)B Substrates, Leo J. Schowalter, Kai Yang, Thomas Thundat

Scanning Microscopy

When homoepitaxial growth is performed on exactly oriented (singular) (111) GaAs substrates, while maintaining the √19 x √19 surface reconstruction, the originally flat surface spontaneously evolves vicinal (111) facets that are tilted approximately 2.5° toward the < 211 > azimuthal directions. These facets form pyramid-like structures where the distance between adjacent peaks can be varied from as little as 1 μm to tens of μm. When these surfaces are observed with atomic force microscopy (AFM), we find that they are extremely smooth with the observed tilt resulting from atomic steps which are spaced at approximately 7.5 nm. We have also studied growth on …

Balancing Surface Energy Terms For Stable Growth Of Planar Surfaces, M. Albrecht, P. O. Hansson, S. Christiansen, W. Dorsch, H. P. Strunk, E. Bauser

Scanning Microscopy

We investigate the driving forces that determine the growth mode of heteroepitaxial Ge layers grown from solution on Si substrates with orientations (001), (011) and (111) by transmission electron microscopy (TEM) and atomic force microscopy (AFM). Using liquid phase epitaxy, we can study the influences of strain and surface energy terms independently on effects due to limited surface diffusion. In (001) and (011) orientated layers, {111} faceted islands form (Stranski-Krastanov growth). In contrast, (111) orientated layers grow in a two-dimensional step flow growth mode (Frank-van der Merwe growth).

We model these investigations in terms of energy minimisation considering surface energy …

Electron Spectroscopy And Atomic Force Microscopy Studies Of Dna Adsorption On Mica, Carol E. Rabke, Lisa A. Wenzler, Thomas P. Beebe Jr.

Scanning Microscopy

Various methods for the deposition of deoxyribonucleic acid (DNA) molecules on mica are investigated to determine their reproducibility, and to quantify their ability to bind DNA. The use of these deposition methods for sample preparation for biological scanning tunneling microscopy (STM) and atomic force microscopy (AFM) studies is discussed. Auger electron spectroscopy (AES) and electron spectroscopy for chemical analysis (ESCA) were used to investigate the quantity of DNA adsorbed. AFM images of DNA deposited using the methods investigated are presented. The combination of AFM results with AES and ESCA results provides a basic understanding of the deposition techniques studied and …

Atomic Force Microscopy Study Of Human Tooth Enamel Surfaces, Ph. Schaad, E. Paris, F. J. G. Cuisinier, J. -C. Voegel

Scanning Microscopy

Human enamel features from individual crystals up to prisms were observed by atomic force microscopy (AFM). Low magnification images of vestibular tooth surfaces show the existence of enamel prisms appearing as deep holes. Individual, parallel enamel crystals show lateral faces elongated and formed by the (100) planes of hydroxyapatite (HA). Height differences between (001) faces create the roughness of enamel surface. Individual (001) crystal faces can be observed clearly at higher magnification and show the characteristic hexagonal shape with 60° angles between (100) faces. This study confirms the applicability of AFM for studying biological hydroxyapatite crystals.

Scanning Tunneling Microscopy: A Chemical Perspective, C. Julian Chen

Scanning Microscopy

In this review article, scanning tunneling microscopy (STM) is presented in a chemical perspective. The typical distance from the nucleus of the apex atom of the tip to the top-layer nuclei of the sample is 4-6 Å, where a strong attractive atomic force, i.e., a partial covalent bond, arises between the tip and the sample. The origin of the covalent bond is the back-and-forth transfer of electrons between two atoms, which Pauling has called resonance. While a bias voltage is applied between them, a net electron current in a specific direction arises. This tunneling current is a result of …

Morphology Studies Of Iron-Manganese Thin Films, G. Mathew, K. -W. Ng, A. R. Sethuraman, J. M. Stencel

Scanning Microscopy

Fe-based catalysts are known to be effective for Fischer-Tropsch synthesis from coal but are sensitive to sulfur poisoning. Addition of manganese to these catalysts has been proposed in an effort to combat this catalyst deactivation. To investigate the fundamental physical aspects of Mn incorporation into Fe, different compositions of model thin films of Fe-Mn, ranging from 100% Fe to 100% Mn were studied for the very first time, using scanning tunneling microscopy (STM), atomic force microscopy (AFM) and scanning electron microscopy. Our preliminary results indicate that the grain size of iron varied from 50 nm to 150 nm using the …

Atomic Force Microscopy Of Dna On Mica And Chemically Modified Mica, T. Thundat, D. P. Allison, R. J. Warmack, G. M. Brown, K. B. Jacobson, J. J. Schrick, T. L. Ferrell

Scanning Microscopy

Atomic force microscopy (AFM) was used to image circular DNA adsorbed on freshly cleaved mica and mica chemically modified with Mg(II), Co(II), La(III), and Zr(IV). Images obtained on unmodified mica show coiling of DNA due to forces involved during the drying process. The coiling or super twisting appeared to be right handed and the extent of super twisting could be controlled by the drying conditions. Images of DNA observed on chemically modified surfaces show isolated open circular DNA that is free from super twisting, presumably due to strong binding of DNA on chemically modified surfaces.

Calibration Of Atomic Force Microscope Tips Using Biomolecules, T. Thundat, X.-Y. Zheng, S. L. Sharp, D. P. Allison, R. J. Warmack, D. C. Joy, T. L. Ferrell

Scanning Microscopy

Atomic force microscope (AFM) images of surfaces and samples mounted on substrates are subject to artifacts such as broadening of structures and ghost images of tips due to the finite size and shape of the contacting probe. Therefore, knowledge of the radius of the AFM probe tip is essential for the interpretation of images. We have deduced the shape of the AFM tip by imaging cylindrical biological molecules of various diameters such as deoxyribonucleic acid (DNA), tobacco mosaic virus (TMV), tobacco etch virus (TEV) and bacteriophage M-13 (M-13). Using a paraboloidal tip model and numerically solving equations of contact, the …

The Scanning Probe Microscope, J. Jahanmir, B. G. Haggar, J. B. Hayes

Scanning Microscopy

Scanning probe microscopy bas evolved into a powerful tool since its inception in 1982. The scanning probe microscope bas found applications in metrology, spectroscopy, and lithography. We will review the background of the technology, discuss the different types of scanning probe microscopes including the scanning tunneling microscope and the scanning force microscope, and present many of the applications for the instrument.

Scanning Tunneling Microscopy And Fabrication Of Nanometer Scale Structures At The Liquid-Gold Interface, J. Schneir, H. H. Harary, J. A. Dagata, P. K. Hansma, R. Sonnenfeld

Scanning Microscopy

The Scanning Tunneling Microscope (STM) can image gold surfaces covered with a variety of liquids. This paper reviews the results obtained using the STM to image gold surfaces covered with liquid. These results include the creation of 10 nm structures, images of the electrochemical process of electroplating, and the production of atomically flat Au (111) surfaces. We conclude that in the future STM will find further application in the area of nanostructure fabrication and electrochemistry. The trend in the field is toward greater control of the electrochemical environment.