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Journal ArticleDOI

Elucidation and Identification of Double-Tip Effects in Atomic Force Microscopy Studies of Biological Structures

27 Jul 2012-Journal of Surface Engineered Materials and Advanced Technology (Scientific Research Publishing)-Vol. 2012, Iss: 3, pp 238-247

TL;DR: The results can serve as a foundation to design computer-based automatic detection of double-tip AFM images during nanoscale measuring and imaging of biomolecules and even non-biological materials or structures, and then personal experience is not needed any longer to evaluate artifactual images induced by the double- Tip/probe effect.

AbstractWhile atomic force microscopy (AFM) has been increasingly applied to life science, artifactual measurements or images can occur during nanoscale analyses of cell components and biomolecules. Tip-sample convolution effect is the most common mechanism responsible for causing artifacts. Some deconvolution-based methods or algorithms have been developed to reconstruct the specimen surface or the tip geometry. Double-tip or double-probe effect can also induce artifactual images by a different mechanism from that of convolution effect. However, an objective method for identifying the double-tip/probe-induced artifactual images is still absent. To fill this important gap, we made use of our expertise of AFM to analyze artifactual double-tip images of cell structures and biomolecules, such as linear DNA, during AFM scanning and imaging. Mathematical models were then generated to elucidate the artifactual double-tip effects and images develop during AFM imaging of cell structures and biomolecules. Based on these models, computational formulas were created to measure and identify potential double-tip AFM images. Such formulas proved to be useful for identification of double-tip images of cell structures and DNA molecules. The present studies provide a useful methodology to evaluate double-tip effects and images. Our results can serve as a foundation to design computer-based automatic detection of double-tip AFM images during nanoscale measuring and imaging of biomolecules and even non-biological materials or structures, and then personal experience is not needed any longer to evaluate artifactual images induced by the double-tip/probe effect.

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Citations
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Journal ArticleDOI
Huanhuan Liao1, Hui He1, Yuan Chen1, Fangfa Zeng1, Jie Huang1, Li Wu1, Yong Chen1 
TL;DR: It is found that the abilities of cell spreading and migration first increased at early passages and then decreased after passage 15, in agreement with the changes in average length of actin filaments, which implies that for pre-stored adherent cells at −80 °C cell passages 5–10 are optimal for in vitro studies.
Abstract: The effects of serial cell passaging on cell spreading, migration, and cell-surface ultrastructures have been less investigated directly. This study evaluated the effects of long-term serial cell passaging (totally 35 passages) on cultured human umbilical vein endothelial cells which were pre-stored at −80 °C as usual. Percentage- and spread area-based spreading assays, measurements of fluorescently labeled actin filaments, migration assay, and measurements of cell-surface roughness were performed and quantitatively analyzed by confocal microscopy or atomic force microscopy. We found that the abilities of cell spreading and migration first increased at early passages and then decreased after passage 15, in agreement with the changes in average length of actin filaments. Recovery from cold storage and effects of cell passaging were potentially responsible for the increases and decreases of the values, respectively. In contrast, the average roughness of cell surfaces (particularly the nucleus-surrounding region) first dropped at early passages and then rose after passage 15, which might be caused by cold storage- and cell passaging-induced endothelial microparticles. Our data will provide important information for understanding serial cell passaging and implies that for pre-stored adherent cells at −80 °C cell passages 5–10 are optimal for in vitro studies.

24 citations


Cites methods from "Elucidation and Identification of D..."

  • ...An Agilent AFM series 5500 (Agilent Technologies, Santa Clara, CA, USA) was recruited to image individual whole cells and cell-surface ultrastructures in tapping mode at room temperature with a lateral scan rate of *0.5 Hz....

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  • ...Therefore, we utilized AFM to image the three regions (Fig....

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  • ...Next, we made use of our expertise of atomic force microscopy (AFM) (Chen 2012; Chen et al. 2011; Jin et al. 2011; Jin et al. 2012) to investigate the effects of cell passaging on cell-surface ultrastructures of HUVECs....

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  • ...Atomic force microscopy (AFM) Cells were plated on sterilized coverslips in the wells of a 6-well plate and cultured in a CO2 incubator at 37 C for 24 h....

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  • ...Keywords Cell passaging Cell spreading Cell migration Cell-surface roughness Actin filaments Atomic force microscopy (AFM) Human umbilical vein endothelial cells (HUVECs)...

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Journal ArticleDOI
TL;DR: This work applies a novel deblurring technique, using a Bayesian framework, to yield a reliable estimation of the real surface topography without any prior knowledge of the tip geometry (blind reconstruction), and focuses specifically on the double-tip effect.
Abstract: The atomic force microscopy (AFM) allows the measurement of interactions at interfaces with nanoscale resolution. Imperfections in the shape of the tip often lead to the presence of imaging artifacts, such as the blurring and repetition of objects within images. In general, these artifacts can only be avoided by discarding data and replacing the probe. Under certain circumstances (e.g., rare, high-value samples, or extensive chemical/physical tip modification), such an approach is not feasible. Here, we apply a novel deblurring technique, using a Bayesian framework, to yield a reliable estimation of the real surface topography without any prior knowledge of the tip geometry (blind reconstruction). A key contribution is to leverage the significant recently successful body of work in natural image deblurring to solve this problem. We focus specifically on the double-tip effect, where two asperities1 are present on the tip, each contributing to the image formation mechanism. Finally, we demonstrate that the proposed technique successfully removes the double-tip effect from high-resolution AFM images, which demonstrate this artifact while preserving feature resolution.1 An asperity is a localized sharp peak in the surface of an object.

7 citations


01 Jan 2017

1 citations


Cites background from "Elucidation and Identification of D..."

  • ...These separate tip protrusions result in duplicates of the same feature: true image and the “ghost” image.(167,158) Double tips typically come from a damaged AFM tip that often results in the formation of additional spikes by dislodging particles during manufacturing, tip use, and through the attachment of surface debris, that often occurs while imaging....

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References
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Journal ArticleDOI
09 Jan 2003-Nature
Abstract: Neat rows of paired photon receptors are caught on camera in their natural state. In vertebrate retinal photoreceptors, the rod outer-segment disc membranes contain densely packed rhodopsin molecules for optimal light absorption and subsequent amplification by the visual signalling cascade1, but how these photon receptors are organized with respect to each other is not known. Here we use infrared-laser atomic-force microscopy to reveal the native arrangement of rhodopsin, which forms paracrystalline arrays of dimers in mouse disc membranes. The visualization of these closely packed rhodopsin dimers in native membranes gives experimental support to earlier inferences about their supramolecular structure2,3 and provides insight into how light signalling is controlled.

732 citations


Journal ArticleDOI
TL;DR: Treatment of the tip-surface interaction as a simple geometrical exclusion allows calculation of many quantities important for SPM dimensional metrology and Blind reconstruction, previously demonstrated only for simulated noiseless images, is here extended to images with noise or other experimental artifacts.
Abstract: To the extent that tips are not perfectly sharp, images produced by scanned probe microscopies (SPM) such as atomic force microscopy and scanning tunneling microscopy are only approximations of the specimen surface. Tip-induced distortions are significant whenever the specimen contains features with aspect ratios comparable to the tip’s. Treatment of the tip-surface interaction as a simple geometrical exclusion

592 citations


"Elucidation and Identification of D..." refers methods in this paper

  • ...At present, some methods or algorithms for reconstruction of specimen surfaces or tip geometries have been developed mainly by deconvolution [28,29]....

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Journal ArticleDOI
05 Jul 2002-Science
TL;DR: This work demonstrated sequence-specific molecular lithography on substrate DNA molecules by harnessing homologous recombination by RecA protein to patterned the coating of DNA with metal, localized labeled molecular objects and grew metal islands on specific sites along the DNA substrate, and generated molecularly accurate stable DNA junctions for patterning theDNA substrate connectivity.
Abstract: Recent advances in the realization of individual molecular-scale electronic devices emphasize the need for novel tools and concepts capable of assembling such devices into large-scale functional circuits. We demonstrated sequence-specific molecular lithography on substrate DNA molecules by harnessing homologous recombination by RecA protein. In a sequence-specific manner, we patterned the coating of DNA with metal, localized labeled molecular objects and grew metal islands on specific sites along the DNA substrate, and generated molecularly accurate stable DNA junctions for patterning the DNA substrate connectivity. In our molecular lithography, the information encoded in the DNA molecules replaces the masks used in conventional microelectronics, and the RecA protein serves as the resist. The molecular lithography works with high resolution over a broad range of length scales from nanometers to many micrometers.

567 citations


"Elucidation and Identification of D..." refers background in this paper

  • ...One of the important research endeavors is to understand nanoscale structures and life events through the nano-measuring and imaging of cells [2-6] or thin sections of them [7], cellular organelles [8], proteins [9-13], polysaccharide [14], DNA [15] and others using the instruments such as scanning tunneling microscopy (STM), near field scanning optical microscope (NSOM) [16-18] and atomic force microscope (AFM) [19-21]....

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Journal ArticleDOI
07 Nov 2003-Science
TL;DR: Instruments with increased imaging rates, lower probe-specimen force interactions, and probe configurations not constrained to planar surfaces are being developed, with the goal of imaging processes at the single-molecule level—not only at surfaces but also within three-dimensional volumes—in real time.
Abstract: Twenty years ago the first scanning probe instrument, the scanning tunneling microscope, opened up new realms for our perception of the world. Atoms that had been abstract entities were now real objects, clearly seen as distinguishable individuals at particular positions in space. A whole family of scanning probe instruments has been developed, extending our sense of touching to the scale of atoms and molecules. Such instruments are especially useful for imaging of biomolecular structures because they can produce topographic images with submolecular resolution in aqueous environments. Instruments with increased imaging rates, lower probe-specimen force interactions, and probe configurations not constrained to planar surfaces are being developed, with the goal of imaging processes at the single-molecule level—not only at surfaces but also within three-dimensional volumes—in real time.

339 citations


"Elucidation and Identification of D..." refers background in this paper

  • ...One of the important research endeavors is to understand nanoscale structures and life events through the nano-measuring and imaging of cells [2-6] or thin sections of them [7], cellular organelles [8], proteins [9-13], polysaccharide [14], DNA [15] and others using the instruments such as scanning tunneling microscopy (STM), near field scanning optical microscope (NSOM) [16-18] and atomic force microscope (AFM) [19-21]....

    [...]


Journal ArticleDOI
21 Jul 2000-Science
TL;DR: A distinct substructure is reported on in the images of individual adatoms on silicon (111)-(7x7), two crescents with a spherical envelope, interpreted as images of two atomic orbitals of the front atom of the tip.
Abstract: The atomic force microscope images surfaces by sensing the forces between a sharp tip and a sample. If the tip-sample interaction is dominated by short-range forces due to the formation of covalent bonds, the image of an individual atom should reflect the angular symmetry of the interaction. Here, we report on a distinct substructure in the images of individual adatoms on silicon (111)-(7x7), two crescents with a spherical envelope. The crescents are interpreted as images of two atomic orbitals of the front atom of the tip. Key for the observation of these subatomic features is a force-detection scheme with superior noise performance and enhanced sensitivity to short-range forces.

319 citations