Nova software

Manufactured by NT-MDT

Nova software is a data acquisition and processing platform developed by NT-MDT. It serves as the control interface for various NT-MDT laboratory equipment, enabling users to collect, analyze, and manage data generated by these instruments.

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Lab products found in correlation

Afm integra vita, by NT-MDT (1 mentions) Dv401 bv, by Oxford Instruments (1 mentions) Integra spectra, by NT-MDT (1 mentions) Ntegra, by NT-MDT (1 mentions) Afm ntegra vita microscope, by NT-MDT (1 mentions)

8 protocols using nova software

AFM Imaging of Globular and Monolayer Biot-CMG-DOPE

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For AFM imaging of a globular form of biot‐CMG‐DOPE, the sample solution was diluted to an appropriate concentration (100 μM) with PBS buffer (pH 7.4). The sample (10 μl) was deposited onto a freshly cleaved mica surface. After 15 min incubation at room temperature, the mica was rinsed three times with 100 μl Milli‐Q water in order to remove salts and unbound material, followed by drying in desiccator for 24 hours. After that, the sample was loaded for AFM imaging. AFM images were obtained at 25 °C and a relative humidity 35 %. Atomic force microscope SFC113LNTF (NT‐MDT, Russia) with silicon probes HA_HR/50 (NT‐MDT, Russia) with resonance frequency 230 kHz were used. The scan rate was 0.78 Hz and the scan size was typically 5 μm. AFM was operated in the tapping mode. Sample imaging and height measurements were done using Nova software (NT‐MDT, Russia).
For AFM imaging of a monolayer form of biot‐CMG‐DOPE, a WITech alpha300 RA system (ULM, Germany) was utilised with an AFM Arrow Cantilever, stiffness is 0.2 N/m, in the tapping mode. To determine the layer thickness, a scan of the surface topography was performed, and a part of the coated and a part of the removed material was captured within an area scan of 10 μm by 10 μm.

Zalygin A., Solovyeva D., Vaskan I., Henry S., Schaefer M., Volynsky P., Tuzikov A., Korchagina E., Ryzhov I., Nizovtsev A., Mochalov K., Efremov R., Shtykova E., Oleinikov V, & Bovin N. (2020). Structure of Supramers Formed by the Amphiphile Biotin‐CMG‐DOPE. ChemistryOpen, 9(6), 641-648.

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Statistical Analysis of Immunoassay Results

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Statistical processing of the results was carried out using Nova software (NT-MDT, Russia) and Microsoft Excel (Microsoft, USA). The data were analyzed using test-test to compare differences between the groups. The consistency of the results for determining the activity of sera and immunoglobulin obtained by the proposed method and neutralization reaction in white mice was calculated by Bland-Altman method 30 (link).

Generalov S.V., Erokhin P.S., Kuznetsov O.S., Abramova E.G., Zhulidov I.M, & Osina N.A. (2021). Determining the Specific Activity of Anti-Rabies Sera and Immunoglobulin Using Atomic Force Microscopy of Cell Cultures. Avicenna Journal of Medical Biotechnology, 13(3), 136-142.

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Dps-DNA Complex Formation Analysis

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Stored solutions of purified Dps were passed through a Sephadex G-15 column (1x5 cm³) to remove any aggregated particles. Collected fractions were diluted in the buffer containing 50 mM Tris-HCl (pH 7.5) and 10 mM NaCl, to the final concentration 1 ng/μl (4.4 nM of dodecamers) and 2 μl of this solution were deposited on mica for scanning. Linear DNA fragments or Y-shape structures were dissolved in 5 mM MgCl₂ to the concentration of 1 ng/μl (4–19 nM). The Dps complexes with different DNA fragments were formed at room temperature in the buffer: 50 mM Tris-HCl (pH 7.5), 10 mM NaCl and 5 mM MgCl₂ (10 μl) for 30 minutes and loaded on mica. Three-ten molar excess of linear DNA fragments or five-fifty molar excess of branched molecules was used for complex formation. Control samples were prepared by the same way, but without Dps. All samples were hold on mica for 5 minutes, washed twice with water for 30 seconds, dried, and the structure of complexes formed was analyzed by AFM Integra-Vita (NT-MDT, Russia) using cantilevers NSG03 with 10 nm tip curvature radius and 47–150 kHz resonance frequency. Measurements were done in semi-contact (tapping) mode. Images obtained were analyzed by Nova software (NT-MDT, Russia).

Melekhov V.V., Shvyreva U.S., Timchenko A.A., Tutukina M.N., Preobrazhenskaya E.V., Burkova D.V., Artiukhov V.G., Ozoline O.N, & Antipov S.S. (2015). Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy. PLoS ONE, 10(5), e0126504.

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Protein Imaging with Atomic Force Microscopy

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AFM measurements were performed as described before [18] (link). Briefly, a drop of a 0.5-0.75 mg/ml protein solution was placed on a freshly cleaved mica sheet and dried immediately with a gentle stream of nitrogen gas. The salt deposits were removed by extensive washing with milli-Q water. The sample was once again dried with nitrogen gas. All images were recorded in air under ambient conditions in semi-contact mode with a scan rate of 0.8 Hz using a SOLVER PRO-M AFM instrument (NTMDT, Moscow). The force was kept at the lowest possible value by continuously adjusting the set-point and feed-back gain during imaging. Image analysis was performed using NOVA software, supplied by NTMDT.

Tarafdar P.K., Vedantam L.V., Sankhala R.S., Purushotham P., Podile A.R, & Swamy M.J. (2014). Oligomerization, Conformational Stability and Thermal Unfolding of Harpin, HrpZPss and Its Hypersensitive Response-Inducing C-Terminal Fragment, C-214-HrpZPss. PLoS ONE, 9(12), e109871.

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Atomic Force Microscopy Protein Imaging

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To prepare samples for AFM 2 µL of solution from the protein sample incubated at 37 °C (with a concentration of 0.1 mg/mL) was taken, the solution was transferred to freshly cleaved mica and incubated for 5 min. The sample was then washed three times in a drop of distilled water for 30 seconds and dried in the air. Similarly, all studied samples were prepared, which were subsequently sampled depending on the incubation time and loaded on mica.
AFM imaging was performed with AFM Integra-Vita microscope (“NT-MDT”, Zelenograd, Russia) in noncontact (tapping) mode in air. The typical scan rate was 1 Hz. Measurements were carried out using cantilevers NSG03 with a resonance frequency of 47–150 kHz and ensured 10 nm tip curvature radius. The processing and presentations of AFM images were performed using Nova software (“NT-MDT”, Zelenograd, Russia) and Gwyddion 2.44 software (Czech Metrology Institute, Brno, Czech Republic).

Timchenko M., Abdullatypov A., Kihara H, & Timchenko A. (2019). Effect of Single Amino Acid Substitutions by Asn and Gln on Aggregation Properties of Bence-Jones Protein BIF. International Journal of Molecular Sciences, 20(20), 5197.

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Topography and Composition Analysis of CHO Cells

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The topography of the CHO cells was evaluated by AFM imaging, and measurements of the cells’ surface roughness were performed using the NT-MDT Solver system from NT-MDT Inc. in semi-contact mode using commercial silicon cantilevers with a tip diameter of 10 nm and force constant of 1.5 N/m. Cell surface roughness analysis was performed on the topography images of cell surface areas (5 × 5 µm) using Nova software from NT-MDT Inc. Surface roughness factors (10-point height (Sz) and average) were determined.
Energy-dispersive X-ray spectroscopy (EDS) analysis was performed to determine the TiO₂-NPs content in CHO cells after exposure to the TiO₂-NP colloidal solution. The samples were examined using a Hitachi S-3400N Type II scanning electron microscope (Tokyo, Japan).
The Raman spectra of CHO cells were registered using a confocal Raman system ‘upright INTEGRA Spectra’ from NT-MDT, using a 100× objective, 20 mW 532 nm wavelength DPSS laser, and a spectrometer—Solar TII from NT-MDT, equipped with a TE-cooled (−60 °C) CCD camera—DV401-BV from Andor Technology (Oxford Instruments, Abingdon, UK). The power of the laser at the sample was 0.4 mW, and the acquisition time was 20 s.

Batiuskaite D., Bruzaite I., Snitka V, & Ramanavicius A. (2022). Assessment of TiO2 Nanoparticle Impact on Surface Morphology of Chinese Hamster Ovary Cells. Materials, 15(13), 4570.

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Atomic Force Microscopy of α-Synuclein Fibrils

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α-Syn fibrils formed in the presence and absence of 500 µM of each studied cation were also analyzed by atomic force microscopy. Briefly, 10 µl of 100 fold diluted α-Syn fibril samples were placed on a freshly cleaved mica and dried at room temperature. Then, the images were obtained in semicontact mode using an Atomic Force Microscopy (NTEGRA, NT-MDT, Russia) followed by processing the images by Nova software (version 1.26.0.1443). For each sample 23–27 measurements were performed.

Atarod D., Mamashli F., Ghasemi A., Moosavi-Movahedi F., Pirhaghi M., Nedaei H., Muronetz V., Haertlé T., Tatzelt J., Riazi G, & Saboury A.A. (2022). Bivalent metal ions induce formation of α-synuclein fibril polymorphs with different cytotoxicities. Scientific Reports, 12, 11898.

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Atomic Force Microscopy of Biopolymer Hydrolysates

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The samples were prepared for AFM as follows. Buffer solution was used to bring the filler concentration to 2.5 mg/mL. Before their use, filler samples were incubated for 40 min at 37 °C. For hydrolysates, an equal volume of the sample was taken from the reaction mixture after 5, 40 and 120 min of incubation at 37 °C. We also analyzed the purified sample of the HPC homogenate diluted 21 times by phosphate buffer after it was incubated for 40 min at 37 °C. Next, two μL of the sample was transferred to freshly cleaved mica and incubated for 5 min. The sample was then washed twice in a drop of distilled water (deionized by a type I Milli-Q system) for 30 s and air-dried. AFM imaging was performed with an AFM Ntegra-Vita microscope (NT-MDT, Russia) in noncontact (tapping) mode in air. The typical scan rate was 0.5–1 Hz. Measurements were carried out using cantilevers NSG03 with a resonance frequency of 47–150 kHz, ensuring a 10 nm tip curvature radius. The processing and presentation of the AFM images were performed using Nova software (NT-MDT, Russia) and Gwyddion 2.44 software (http://gwyddion.net/, Czech Republic).

Ponomareva T., Sliadovskii D., Timchenko M., Molchanov M., Timchenko A, & Sogorin E. (2020). The effect of hepatopancreas homogenate of the Red king crab on HA-based filler. PeerJ, 8, e8579.

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