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Jpk nanowizard 2

Manufactured by Bruker
Sourced in Germany

The JPK Nanowizard II is a high-resolution atomic force microscope (AFM) designed for advanced nanoscale imaging and analysis. It provides precise control and measurement capabilities at the nanometer scale. The core function of the Nanowizard II is to enable researchers to investigate the topography and properties of surfaces and materials with exceptional resolution and accuracy.

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17 protocols using jpk nanowizard 2

1

Probing Extracellular Matrix Stiffness via AFM

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Atomic force microscopy (AFM) measurements of extracellular matrix stiffness were performed on freshly cut 16 μm thick cryosections using the JPK Nano Wizard 2 (Bruker Nano) AFM mounted on an Olympus IX73 inverted fluorescent microscope (Olympus) and operated using the JPK SPM control software v.5. Briefly, cryosections were equilibrated in PBS supplemented with protease inhibitors and measurements were performed within 20 min of thawing the samples. Silicon Nitride cantilevers with 3.5 μm colloidal particle (NanoAndMore GbmbH) were used for the nanoindentation experiments. For all of the indentation experiments, forces of up to 2 nN were applied, and the velocities of cantilever approach and retraction were kept constant at 2 μm /second. Before fitting the Hertz model corrected by the tip geometry to obtain Young’s Modulus (Poisson’s ratio of 0,5), the offset was removed from the baseline, the contact point was identified, and cantilever bending was subtracted from all force curves.
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2

Nanomechanical Profiling of Cell Monolayers

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AFM measurements were performed on cell monolayers plated on silicon elastomers using JPK NanoWizard 2 (Bruker Nano) atomic force microscope mounted on an Olympus IX73 inverted fluorescent microscope (Olympus) and operated via JPK SPM Control Software v.5. Elastomers were mounted on the AFM directly after cyclic stretch and measurements were performed within 15 minutes. Triangular non-conductive Silicon Nitride cantilevers (MLCT, Bruker Daltonics) with a nominal spring constant of 0.01 Nm−1 were used for the nanoindentation experiments of the apical surface of cells and the nucleus. For all indentation experiments, forces of up to 3 nN were applied, and the velocities of cantilever approach and retraction were kept constant at 2 μm s−1 ensuring an indentation depth of 500nm. All analyses were performed with JPK Data Processing Software (Bruker Nano). Prior to fitting the Hertz model corrected by the tip geometry to obtain Young’s Modulus (Poisson’s ratio of 0.5), the offset was removed from the baseline, contact point was identified, and cantilever bending was subtracted from all force curves.
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3

Elastic Properties of Cells via AFM Measurements

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AFM measurements were performed on micropatterns generated on glass bottom dishes (35 mm Ibidi). Measurements were done using a JPK NanoWizard 2 (Bruker Nano) atomic force microscope mounted on an Olympus IX73 inverted fluorescent microscope (Olympus) and operated via JPK SPM Control Software v.5. Spherical silicon dioxide beads with a diameter of 3.5 μm glued onto tipless silicon nitride cantilevers (NanoAndMore, CP-PNPL-SiO-B-5) with a nominal spring constant of 0.08 N m−1 were used. For all indentation experiments, forces of up to 4 nN were applied, and the velocities of cantilever approach and retraction were kept constant at 2 μm s−1 ensuring detection of elastic properties only. All analyses (>50 cells per experiment/condition) were performed with JPK Data Processing Software (Bruker Nano). Prior to fitting the Hertz model to obtain cell Young’s Modulus (Poisson’s ratio of 0.5), the offset was removed from the baseline, contact point was identified, and cantilever bending was subtracted from all force curves.
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4

AFM Imaging of Glass Surface Topology

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Atomic force microscopy (AFM) is widely used for high-resolution imaging of sample surfaces and for studying the properties of glass surfaces.27–30 AFM imaging of the surface topology of soda-lime glass before and after the cleaning process was done using AFM (JPK Nanowizard II, Bruker, Billerica, Massachusetts, USA) in intermittent contact mode with a line rate of 0.7–0.9 Hz, with the HQ:NSC14/AL BS AFM probes from μMasch (resonance freq. 160 kHz). The height profiles of the AFM images are shown as cross sections in part B of Fig. 5 and 6. The Gwyddion software31 was used for surface roughness (RS) analysis of the AFM images. In Gwyddion, RS is expressed as the mean square roughness (RMS) of height irregularities which is calculated using the 2nd central moment of the data values.31 2D FFT filtering was used to remove background noise and the plane background was also removed to properly level the images.31 All data analysis was performed on images after applying only the mentioned filters to best preserve the raw data while eliminating the impact of noise and unleveled background.
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5

Atomic Force Microscopy for Surface Roughness

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Surface roughness was assessed using an atomic force microscope (JPK Nanowizard II, Bruker, Germany) (Figure S2b). The surface roughness parameters recorded were (a) Ra (roughness average), the arithmetic average of the absolute values of the profile heights over the evaluation length, and (b) Rq (RMS roughness), the root mean square (RMS) average of the profile heights over the evaluation length. Measurements were randomly taken at multiple sample points and then the mean was calculated.
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6

Measuring Cellular Adhesion and Lipid Interactions

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All crystals were glued to cantilever (Arrow TL- 1, Nanoworld) with epoxy (21 (link)) at least 12 h before use. All attraction forces between cell and crystal were measured with JPK CellHesion (JPK) (23 (link)). Briefly, the measurement was carried in the relative force feedback contact/tapping mode (IP gain: 50 Hz; IG gain: 0.001 Hz; correct baseline: 1; relative set point: 0.5 nN; z length: 50 µm; extend delay: 0 s; constant height). Data were analyzed with JPK Data Processing. Maximum binding forces were calculated and plotted. Each dot presents a single measurement.
Attraction forces between crystal and lipid monolayer were measured with JPK NanoWizard II (JPK). All set up was the same as the JPK CellHesion except z length was 10 µm. AFM scanning mode was used to confirm domain formation.
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7

Atomic Force Microscopy of pDR1m Samples

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An atomic force microscope JPK NanoWizard II (JPK Instruments) was used to acquire images of pDR1m samples. An Axio Observer Z1 microscope (Zeiss) was combined with the AFM to control tips and sample position. Silicon nitride probes (MLCT, Bruker), with a spring constant of 0.01 N/m, were used in contact mode, in air, and at room temperature. Raw images were corrected by the JPK data processing software using a standard procedure (flatten, plane-fit, and artifact lines caused by the tip attachment and removal). The scale indicating the sample height or deflection was adjusted to limit the gap between high and low regions.
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8

Characterization of PEG-Arg@IONPs

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The internal structure of PEG-Arg@IONPs was studied through transmission electron microscope (Cambridge 360–1990 Stereo Scan Instrument-EDS) measurements.
Morphology of PEG-Arg@IONPs was studied by atomic force microscopy (AFM) (JPK Nano wizard II, JPK instrument, Bouchestrasse, Berlin, Germany) in an intermittent contact mode.
X-ray diffraction was measured by a Bruker AXS model D8 Advance powder X-ray diffractometer.
FTIR spectra of the sample were measured by a Bruker, Tensor 27 FTIR spectrophotometer.
To evaluate the behavior in reaction to the increased temperature, thermogravimetric analysis (TGA, Linseis Instruments model, STA PT 1000, USA) and also, differential scanning calorimetry (DSC, Mettler Toledo, model Star SW 9.30, Schwerzenbach, Switzerland) were used.
Sample magnetization curves were attained by means of a vibrating sample magnetometer (VSM Magnetic Daghigh Daneshpajouh Co, Kashan, Iran).
ζ-potential and hydrodynamic size measurements were done using a nano/zetasizer (Malvern Instruments, Worcestershire, UK, model Nano ZS).
To quantify the stability of PEG-Arg@IONPs nanoparticles dispersed in water, DMEM, and saline, respectively, UV-visible absorbance at 450 nm were used in order to monitor the absorbance of the corresponding dispersion solution containing PEG-Arg@IONPs nanoparticles at a fixed wavelength similar to that in the reported study.
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9

Mechanical Unfolding of Outer Membrane Proteins

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Mechanical unfolding of Omps was performed as described44 (link). Briefly, 1 µL of OMV solution was adsorbed to freshly cleaved mica supports in 75 µL DPBSS for 20 min at room temperature. Samples were washed with DPBSS several times. All AFM measurements were performed on a JPK NanoWizard II (JPK Instruments) using OMCL-RC800PSA cantilevers (Olympus). Cantilevers were calibrated using the thermal noise method64 (link). Adsorbed OMVs were located by imaging in contact mode, followed by force spectroscopy measurements using a contact force of ≈750 pN for 0.5 s, followed by retraction at constant velocity of 2 µm s–1. SMFS experiments were performed over several days, using a new sample and new AFM cantilever every day
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10

Enamel Surface Topography Characterization by AFM

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The topographic characteristics of the enamel surface were assessed using AFM. One sample of each group was used for AFM (JPK Nanowizard II apparatus, JPK Instruments, Berlin, Germany) in tapping mode along with a nonconductive silicon nitrite cantilever (Acta-Probe, APPNano, CA, USA) and a piezoelectric scanner. Scanning frequency was 1 Hz and the spring constant was 13 N/m. The mean surface roughness was measured in five areas (each measuring 5 × 5 μm) using the formula below [23 (link)]. The results were recorded in nanometres (nm).
Ra=1Ni=1NZiZ¯
Where N is the number of points assessed and Zi-Z is the height relative to the middle surface [23 (link)]. The mean hardness was calculated for each sample.
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