Background correction in scanning probe microscope recordings of macromolecules

Starink, J. P. P.; Jovin, Thomas M.

doi:10.1016/0039-6028(96)00367-6

Cited by 15 publications

(9 citation statements)

References 31 publications

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“…Additional materials and methods, 17 figures, and references (53)(54)(55)(56) are available at http://www.biophysj.org/biophysj/supplemental/S0006-3495(12) 00168-3.…”

Section: Supporting Materialsmentioning

confidence: 99%

Supramolecular Non-Amyloid Intermediates in the Early Stages of α-Synuclein Aggregation

Fauerbach

Yushchenko

Shahmoradian

et al. 2012

Biophysical Journal

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The aggregation of α-synuclein is associated with progression of Parkinson's disease. We have identified submicrometer supramolecular structures that mediate the early stages of the overall mechanism. The sequence of structural transformations between metastable intermediates were captured and characterized by atomic force microscopy guided by a fluorescent probe sensitive to preamyloid species. A novel ~0.3-0.6 μm molecular assembly, denoted the acuna, nucleates, expands, and liberates fibers with distinctive segmentation and a filamentous fuzzy fringe. These fuzzy fibers serve as precursors of mature amyloid fibrils. Cryo-electron tomography resolved the acuna inner structure as a scaffold of highly condensed colloidal masses interlinked by thin beaded threads, which were perceived as fuzziness by atomic force microscopy. On the basis of the combined data, we propose a sequential mechanism comprising molecular, colloidal, and fibrillar stages linked by reactions with disparate temperature dependencies and distinct supramolecular forms. We anticipate novel diagnostic and therapeutic approaches to Parkinson's and related neurodegenerative diseases based on these new insights into the aggregation mechanism of α-synuclein and intermediates, some of which may act to cause and/or reinforce neurotoxicity.

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“…Additional materials and methods, 17 figures, and references (53)(54)(55)(56) are available at http://www.biophysj.org/biophysj/supplemental/S0006-3495(12) 00168-3.…”

Section: Supporting Materialsmentioning

confidence: 99%

Supramolecular Non-Amyloid Intermediates in the Early Stages of α-Synuclein Aggregation

Fauerbach

Yushchenko

Shahmoradian

et al. 2012

Biophysical Journal

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“…This is usually removed in an image flattening step which includes, at least in part, a line-wise component. A method for combining an area-wise surface fit with line-wise flattening in a least squares approach has recently been proposed [ 34 ]. Inclusion of linewise flattening is particularly important when performing a blind tip reconstruction, for otherwise the sharp steps from one line to the next might be mistaken as indicating similar sharp features on the tip.…”

Section: A Practical Guidementioning

confidence: 99%

Algorithms for scanned probe microscope image simulation, surface reconstruction, and tip estimation

Villarrubia¹

1997

J. Res. Natl. Inst. Stand. Technol.

621

497

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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 allows calculation of many quantities important for SPM dimensional metrology. Algorithms for many of these are provided here, including the following: (1) calculating an image given a specimen and a tip (dilation), (2) reconstructing the specimen surface given its image and the tip (erosion), (3) reconstructing the tip shape from the image of a known “tip characterizer” (erosion again), and (4) estimating the tip shape from an image of an unknown tip characterizer (blind reconstruction). Blind reconstruction, previously demonstrated only for simulated noiseless images, is here extended to images with noise or other experimental artifacts. The main body of the paper serves as a programmer’s and user’s guide. It includes theoretical background for all of the algorithms, detailed discussion of some algorithmic problems of interest to programmers, and practical recommendations for users.

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“…Further image processing and analysis were performed with the image processing package SCIL-Image (University of Amsterdam; Technical University of Delft, NL). Background processing was performed according to a procedure described elsewhere (Starink & Jovin, 1996). The height and width of the DNA were determined from sections perpendicular to the contour line of the DNA filament.…”

Section: Methodsmentioning

confidence: 99%

Shear force imaging of DNA in a near‐field scanning optical microscope (NSOM)

Kirsch

Meyer

Jovin

1997

Journal of Microscopy

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SummaryA near-field scanning optical module has been constructed as an accessory for a Nanoscope IIIa commercial scanning probe microscope. Distance feedback and topographic registration are accomplished with an uncoated optical fibre scanning tip by implementation of the shear force technique. The tip is driven by a piezoelectric actuator at a resonance frequency of 8-80 kHz. A laser diode beam is scattered by the tip and detected by a split photodiode, with lock-in detection of the difference signal. The amplitude (r) and phase (v) responses were characterized as a function of the calibrated tip-sample separation. Using an r cos v feedback signal, imaging of pUC18 relaxed circular plasmid DNA spread on mica precoated with cetylpyridinium chloride was achieved. The apparent width (28 Ϯ 5 nm) was approximately four times that achieved by scanning force measurements with the same instrument; the apparent height of the DNA (0 : 6 Ϯ 0 : 3 nm) was similar with the two techniques. These results demonstrate the applicability of the shear force signal for imaging biological macromolecules according to topography and in conjunction with the optical signals of a near-field scanning optical microscope (NSOM).

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Background correction in scanning probe microscope recordings of macromolecules

Cited by 15 publications

References 31 publications

Supramolecular Non-Amyloid Intermediates in the Early Stages of α-Synuclein Aggregation

Supramolecular Non-Amyloid Intermediates in the Early Stages of α-Synuclein Aggregation

Algorithms for scanned probe microscope image simulation, surface reconstruction, and tip estimation

Shear force imaging of DNA in a near‐field scanning optical microscope (NSOM)

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