Tag Archives: life sciences

Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences

Correlating data from different microscopy techniques holds the potential to discover new facets of signalling events in cellular biology.*

In the article “Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences” Ana I. Gómez-Varela, Dimitar R. Stamov, Adelaide Miranda, Rosana Alves, Cláudia Barata-Antunes, Daphné Dambournet, David G. Drubin, Sandra Paiva and Pieter A. A. De Beule report for the first time a hardware set-up capable of achieving simultaneous co-localized imaging of spatially correlated far-field super-resolution fluorescence microscopy and atomic force microscopy, a feat only obtained until now by fluorescence microscopy set-ups with spatial resolution restricted by the Abbe diffraction limit.*

The authors detail system integration and demonstrate system performance using sub-resolution fluorescent beads and applied to a test sample consisting of human bone osteosarcoma epithelial cells, with plasma membrane transporter 1 (MCT1) tagged with an enhanced green fluorescent protein (EGFP) at the N-terminal.*

The simultaneous operation of AFM and super-resolution fluorescence microscopy technique provides a powerful observational tool on the nanoscale, albeit data acquisition is typically obstructed by a series of integration problems. The authors of the above-mentioned article believe that the combination of SR-SIM with AFM presents one of the most promising schemes enabling simultaneous co-localized imaging, allowing the recording of nanomechanical data and cellular dynamics visualization at the same time.*

For measurements on cells in liquid NANOSENSORS™ uniqprobe qp-BioAC-CI AFM probes ( CB1 ) with a nominal resonance frequency of 90 kHz (in air), spring constant of 0.3 Nm−1, partial gold coating on the detector side, and quartz-like circular symmetric hyperbolic (double-concaved) tips with ROC of 30 nm were used. The corresponding AFM areas for the cell images were acquired with a Z-cantilever velocity of 250 μms−1 at a max Z-length of 1.5 μm, resulting in an acquisition time (based on the number of pixels) for Figs. 2, 3, 4 of ca. 13, 8 and 15 min respectively.*

Figure 4 a and b from Ana I. Gómez-Varela et al “Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences :  Simultaneous SR-SIM/AFM acquisition. The AFM measurements were carried out on fixed U2OS cells in medium/buffer with (a) and without N-SIM illumination (b). For convenience and enhanced feature/noise contrast, both AFM topography images in the SR-SIM/AFM overlays are displayed with an edge detection algorithm using a pixel difference operator in X. The topography images from Petri dish surface on three positions (labelled in the figures) were planefit (1st order polynomial function) to compensate for tilts in the sample surface, and subjected to surface roughness analysis Please have a look at the full article to view the full figure. https://rdcu.be/b4Iot
Figure 4 a and b from Ana I. Gómez-Varela et al “Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences : Simultaneous SR-SIM/AFM acquisition. The AFM measurements were carried out on fixed U2OS cells in medium/buffer with (a) and without N-SIM illumination (b). For convenience and enhanced feature/noise contrast, both AFM topography images in the SR-SIM/AFM overlays are displayed with an edge detection algorithm using a pixel difference operator in X. The topography images from Petri dish surface on three positions (labelled in the figures) were planefit (1st order polynomial function) to compensate for tilts in the sample surface, and subjected to surface roughness analysis. Please have a look at the full article to view the full figure. https://rdcu.be/b4Iot

*Ana I. Gómez-Varela, Dimitar R. Stamov, Adelaide Miranda, Rosana Alves, Cláudia Barata-Antunes, Daphné Dambournet, David G. Drubin, Sandra Paiva and Pieter A. A. De Beule
Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences
Nature Scientific Reports volume 10, Article number: 1122 (2020)
DOI: https://doi.org/10.1038/s41598-020-57885-z

Please follow this external link to read the full article https://rdcu.be/b4Iot

Open Access: The article “Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences” by Ana I. Gómez-Varela, Dimitar R. Stamov, Adelaide Miranda, Rosana Alves, Cláudia Barata-Antunes, Daphné Dambournet, David G. Drubin, Sandra Paiva and Pieter A. A. De Beule is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices

MeCP2 and MBD2 are members of a family of proteins that possess a domain that selectively binds 5-methylcytosine in a CpG context. Members of the family interact with other proteins to modulate DNA packing. Stretching of DNA–protein complexes in nanofluidic channels with a cross-section of a few persistence lengths allows us to probe the degree of compaction by proteins.*

In the article “DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices” Ming Liu, Saeid Movahed, Saroj Dangi, Hai Pan, Parminder Kaur, Stephanie M. Bilinovich, Edgar M. Faison, Gage O. Leighton, Hong Wang, David C. Williams Jr. and Robert Riehn demonstrate DNA compaction by MeCP2 while MBD2 does not affect DNA configuration. By using atomic force microscopy (AFM), they determined that the mechanism for compaction by MeCP2 is the formation of bridges between distant DNA stretches and the formation of loops.*

Despite sharing a similar specific DNA-binding domain, the impact of full-length 5-methylcytosine-binding proteins can vary drastically between strong compaction of DNA and no discernible large-scale impact of protein binding. The authors of the article demonstrate that ATTO 565-labeled MBD2 is a good candidate as a staining agent for epigenetic mapping.*

For atomic force microscopy (AFM), the authors used a 7,163-bp linear DNA substrate which contains a 1,697-bp methylated CpG-rich region that is flanked by 2,742-bp and 2,724-bp CpG-free regions. For MeCP2, the DNA substrate and the protein were diluted in AFM imaging buffer (HEPES 20 mM, Mg(OAc)210mM, NaCl 100mM, pH 7.5), mixed together and deposited on freshly peeled mica. For MBD2FLsc, the authors describe how they first mixed the protein and DNA and then diluted the sample in AFM buffer before deposition. The final MeCP2 concentration deposited on mica was 7.5nM, and the MBD2FLsc concentration was 14nM. The mica samples were then washed with filtered deionized water and dried with nitrogen.*

NANOSENSORS™ PointProbe® Plus PPP-FMR AFM probes ( ≈2.8N/m) were used to image the sample at a scan resolution of 5.9nm and a scan rate of 3μm/s.*

Figure 6 from “DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices “ by Ming Liu et al.:
Atomic force microscopy (AFM) of methylated substrates under various conditions. AFM of bare methylated dsDNA oligomer a, the same oligomer with MBD2Flsc b, and with MeCP2 c. Scale bars are 200nm. The green arrows point at ends, and cyan arrows point at loops. The inset in d illustrates the counting method for loops. The distribution of number of free ends (d) and the distribution of number of loops (e) for DNA or DNA–protein complexes was determined from such images (bare DNA N=118, MBD2FLsc N=98, MeCP2 N=108). f Height of isolated DNA–DNA crossings (bare DNA N=52, MBD2FLsc N=68, MeCP2 N=83)

*Ming Liu, Saeid Movahed, Saroj Dangi, Hai Pan, Parminder Kaur, Stephanie M. Bilinovich, Edgar M. Faison, Gage O. Leighton, Hong Wang, David C. Williams Jr. and Robert Riehn
DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices
Epigenetics & Chromatin volume 13, Article number: 18 (2020)
DOI: https://doi.org/10.1186/s13072-020-00339-7

Please follow this external link to read the full article: https://rdcu.be/b3iTm

Open Access: The article “DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices” by Ming Liu, Saeid Movahed, Saroj Dangi, Hai Pan, Parminder Kaur, Stephanie M. Bilinovich, Edgar M. Faison, Gage O. Leighton, Hong Wang, David C. Williams Jr. and Robert Riehn is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Nonlinear Biomechanical Characteristics of Deep Deformation of Native RBC Membranes in Normal State and under Modifier Action

The mechanical properties and structural organization of membranes determine the functional state of red blood cells (RBCs). Deformability is one of the key physiological and biophysical indicators of RBC. Changes of the mechanical characteristics of cell membranes can lead to a decrease in the rate of capillary blood flow and to development of stagnant phenomena in the microcirculation, and it can also reduce the amount of oxygen delivered to the tissues.*

In the article “Nonlinear Biomechanical Characteristics of Deep Deformation of Native RBC Membranes in Normal State and under Modifier Action” Elena Kozlova, Aleksandr Chernysh, Ekaterina Manchenko, Viktoria Sergunova and Viktor Moroz describe how they evaluated the ability of membranes of native human red blood cells (RBCs) to bend into the cell to a depth comparable in size with physiological deformations using the methods of atomic force microscopy ( AFM ) and atomic force spectroscopy ( AFS ).*

As a true estimation of the elastic properties of RBC membranes can be obtained only by measurement of native cell properties the aim of the experiments was to study nonlinear mechanical characteristics of deep deformation of native RBC membranes in normal state and under the action of modifiers, in vitro to make sure that the result would be the closest to the characteristics of a living biological object.*

NANOSENSORS™ rounded AFM tips of the type SD-R150-T3L450B with a typical tip radius of 150 nm from the NANOSENSORS Special Developments List were used to measure the deformation of the RBC membrane by atomic force spectroscopy ( AFS ).*


Figure 5.2. (c) from “Nonlinear Biomechanical Characteristics of Deep Deformation of Native RBC Membranes in Normal State and under Modifier Action “ by Elena Kozlova et al.:
 Bending of membranes under the action of force F for stiff (1) and soft (2) membranes; F is the force acting on the membrane from the probe, Z is the vertical displacement of the piezoscanner, h is the depth of the membrane bending into RBC, PBS is the phosphate buffer solution, and rd is the bending radius of the membrane.

*Elena Kozlova, Aleksandr Chernysh, Ekaterina Manchenko, Viktoria Sergunova, and Viktor Moroz
Nonlinear Biomechanical Characteristics of Deep Deformation of Native RBC Membranes in Normal State and under Modifier Action
Scanning, Volume 2018, Article ID 1810585, 13 pages
Doi: https://doi.org/10.1155/2018/1810585

Please follow this external link to read the full article: https://www.hindawi.com/journals/scanning/2018/1810585/

Open Access The article « Nonlinear Biomechanical Characteristics of Deep Deformation of Native RBC Membranes in Normal State and under Modifier Action ” by Elena Kozlova, Aleksandr Chernysh, Ekaterina Manchenko, Viktoria Sergunova, and Viktor Moroz is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.