Tag: HS AFM

Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC

Long double-stranded (ds) RNA is emerging as a novel alternative to chemical and genetically-modified insect and fungal management strategies. The ability to produce large quantities of dsRNA in either bacterial systems, by in vitro transcription, in cell-free systems or in planta for RNA interference applications has generated significant demand for the development and application of analytical tools for analysis of dsRNA.*

In their article “Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC” Alison O. Nwokeoji, Sandip Kumar, Peter M. Kilby, David E. Portwood, Jamie K. Hobbs and Mark J. Dickman have utilised atomic force microscopy (AFM) in conjunction with ion-pair reverse-phase high performance liquid chromatography (IP-RP-HPLC) to provide novel insight into dsRNA for RNAi applications.*

The AFM analysis enabled direct structural characterisation of the A-form duplex dsRNA and accurate determination of the dsRNA duplex length.*

The work presented in this study demonstrates the ability of AFM in conjunction with IP RP HPLC to rapidly assess sample heterogeneity and provide important structural information regarding dsRNA.*

For the high resolution images presented in Fig. 1(A, B) and 2(B) in the article NanoWorld Ultra-Short Cantilevers USC-F1.2-k0.15 with a High Density Carbon tip (nominal values: tip radius 10 nm, cantilever length 7 μm, stiffness 0.15 N m−1, resonant frequency 1200 kHz in air) were tuned to 600–650 kHz, oscillated at a free amplitude of <30 mV and scanned at a rate of 0.4–1.0 μm s−1,to visualize the dsRNA and dsDNA grooves.*


Fig. 1 A and B from “Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC” by Alison O. Nwokeoji et al. :
Analysis of dsRNA monomers, multimers and higher order assemblies under non-denaturing conditions. Non-denaturing gel electrophoretograms (A) in vivo synthesised dsRNA (521 bp and 698 bp) (B) in vitro synthesised dsRNA (504 bp). Each dsRNA sample was run in duplicate. The proposed dsRNA multimers or higher order assemblies with reduced electrophoretic mobility are highlighted above the corresponding dsRNA main band.

*Alison O. Nwokeoji, Sandip Kumar,Peter M. Kilby, David E. Portwood, Jamie K. Hobbs and Mark J. Dickman
Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC
Analyst, 2019,144, 4985
DOI: 10.1039/c9an00954j

Please follow this external link for the full article: https://pubs.rsc.org/en/content/articlelanding/2019/an/c9an00954j

Open Access: The article « Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC  by Alison O. Nwokeoji, Sandip Kumar,Peter M. Kilby, David E. Portwood, Jamie K. Hobbs and Mark J. Dickman is licensed under a Creative Commons Attribution 3.0 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 https://creativecommons.org/licenses/by/3.0/.

Direct Observation of Long-Chain Branches in a Low-Density Polyethylene

The properties of a polymer change significantly depending on the structure of the polymer chain, particularly, with branched structures, depending on the number of branches and the length of the branch.* However, the long-chain branch (LCB) structure of polyethylene was unclear, due particularly to the complex polymer structure and the limitations of its analysis methods.

In their study “Direct Observation of Long-Chain Branches in a Low-Density Polyethylene” Ken-ichi Shinohara, Masahiro Yanagisawa and Yuu Makida measured the chain length of LCBs and the distance between branch points of LDPE by atomic force microscopy.*

The article mentions the use of NanoWorld Ultra-Short Cantilevers (USC) for high speed atomic force microscopy ( AFM probe type USC-F1.2-k0.15 ) for the single-molecule imaging by atomic force microscopy .*

Figure 1 from “Direct Observation of Long-Chain Branches in a Low-Density Polyethylene “ by K. Shinohara et al.: Direct measurement of LCB in a tubular LDPE (F200-0 fractionated). (A) AFM image of a single molecule of LDPE on mica in DMTS at 25 °C. X: 279 nm, Y: 209 nm, Z: 18 nm. (B) Length of each chain of LDPE. (C) A wire model of self-shrinking structure of polymer chain of LDPE. Main chain: red wire. LCB: black wire. The model was created to be one tenth of the length of the extended chain based on AFM observation (B), MD simulation (Fig. S1), and the molecular weight determined by SEC-MALLS-Visc experiments (see Fig. 2).
Figure 1 from “Direct Observation of Long-Chain Branches in a Low-Density Polyethylene “ by K. Shinohara et al.: Direct measurement of LCB in a tubular LDPE (F200-0 fractionated). (A) AFM image of a single molecule of LDPE on mica in DMTS at 25 °C. X: 279 nm, Y: 209 nm, Z: 18 nm. (B) Length of each chain of LDPE. (C) A wire model of self-shrinking structure of polymer chain of LDPE. Main chain: red wire. LCB: black wire. The model was created to be one tenth of the length of the extended chain based on AFM observation (B), MD simulation (Fig. S1), and the molecular weight determined by SEC-MALLS-Visc experiments (see Fig. 2).

*Ken-ichi Shinohara, Masahiro Yanagisawa, Yuu Makida
Direct Observation of Long-Chain Branches in a Low-Density Polyethylene
Nature Scientific Reportsvolume 9, Article number: 9791 (2019)
doi: https://doi.org/10.1038/s41598-019-46035-9

Please follow this external link for the full article: https://rdcu.be/bJY7S

Open Access: The article «Direct Observation of Long-Chain Branches in a Low-Density Polyethylene» by Ken-ichi Shinohara, Masahiro Yanagisawa and Yuu Makida 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/.

IgA tetramerization improves target breadth but not peak potency of functionality of anti-influenza virus broadly neutralizing antibody

Mucosal immunoglobulins comprise mainly secretory IgA antibodies (SIgAs), which are the major contributor to pathogen-specific immune responses in mucosal tissues. SIgAs exist as mainly dimers and tetramers and play critical roles in mucosal immune responses against influenza.*

Detailed characterization of these anti-viral SIgA is important for better understanding of the mechanisms underlying anti-viral immunity.*
In their article “IgA tetramerization improves target breadth but not peak potency of functionality of anti-influenza virus broadly neutralizing antibody” Saito S, Sano K, Suzuki T, Ainai A, Taga Y, Ueno T, et al. (2019) describe a means of generating a recombinant tetrameric monoclonal SIgA to enable exhaustive characterization of tetrameric SIgAs.
The tetrameric monoclonal SIgA possessing variable regions of anti-influenza viruses broadly neutralizing antibody show that tetramerization of SIgA improves target breadth, but not the peak potency, of their anti-viral functions.*
These results broaden the knowledge about the fundamental role of SIgA tetramerization in anti-viral humoral response at the human respiratory mucosa.*

The high speed atomic force microscopy ( HS-AFM ) experiments mentioned in the article were performed using a NanoWorld Ultra-Short Cantilever USC-F1.2-k0.15.

Fig 1. Production of recombinant tetrameric monoclonal SIgAs. (A) Recombinant monoclonal IgA antibodies purified from the culture supernatant of cells co-transfected with A1+L (left upper), A1+L+J (left lower), A1+L+J+SC (right upper), or A2m2+L+J+SC (right lower), were subjected to size exclusion chromatography (SEC) analysis. A chromatogram showing absorbance at 280 nm revealed three major peaks: peak A (retention volume around 10.4 ml), peak B (retention volume around 9.3 ml), and peak C (retention volume around 8.4 ml). Data are representative of three independent experiments. (B) SDS-PAGE and BN-PAGE analysis of IgG and IgA1/IgA2m2 in each peak fraction (peak A, B, and C) purified from cells co-expressing SC (A1+L+J+SC or A2m2+L+J+SC). (C, D, E) High-mass MALDI-TOF MS analysis of the each peak fraction containing recombinant IgA1 purified from the culture supernatant of cells transfected with A1, L, J, and SC. (C) One main peak (arrow) corresponding to monomer (Mo) was detected in the peak A fraction. (D) Two main peaks (arrows) corresponding to a dimer (Di) and a di-cation dimer (Di2+) were detected in the peak B fraction. (E) Three main peaks (arrows) corresponding to a tetramer (Te), trimer (Tr), and di-cation tetramer (Te2+) were detected in the peak C fraction. (F, G) High-mass MALDI-TOF MS analysis of the each peak fraction of recombinant IgA2m2 purified from the culture supernatant from cells transfected with A2m2, L, J, and SC. (F) One main peak (arrow) corresponding to a monomer (Mo) was detected in the peak A fraction. (G) Three main peaks (arrows) corresponding to a tetramer (Te), a trimer (Tr), and a di-cation tetramer (Te2+) were detected in the peak C fraction. (H) Quantification of the amount of each subunit within the peak B or C fraction of recombinant SIgA1 or SIgA2m2 antibodies purified from the culture supernatant of cells transfected with A1/L/J,/SC or A2m2/L/J/SC using LC-MS with stable isotope-labeled standard peptides. The abundance of each subunit to that of J chain is expressed as a ratio. Data are expressed as box-and-whisker plot with minimum, maximum, median, upper and lower quartiles (n = 6–7). (I) HS-AFM image of peak C derived from a recombinant SIgA1 (A1Te) or SIgA2m2 (A2m2Te) antibody purified from the culture supernatant of cells transfected with A1/L/J/SC or A2m2/L/J/SC. Scale bar, 20 nm.

Fig 1. Production of recombinant tetrameric monoclonal SIgAs from ”
IgA tetramerization improves target breadth but not peak potency of functionality of anti-influenza virus broadly neutralizing antibody ” by
Saito S, Sano K, Suzuki T, Ainai A, Taga Y, Ueno T, et al. (2019) :
 
(A) Recombinant monoclonal IgA antibodies purified from the culture supernatant of cells co-transfected with A1+L (left upper), A1+L+J (left lower), A1+L+J+SC (right upper), or A2m2+L+J+SC (right lower), were subjected to size exclusion chromatography (SEC) analysis. A chromatogram showing absorbance at 280 nm revealed three major peaks: peak A (retention volume around 10.4 ml), peak B (retention volume around 9.3 ml), and peak C (retention volume around 8.4 ml). Data are representative of three independent experiments. (B) SDS-PAGE and BN-PAGE analysis of IgG and IgA1/IgA2m2 in each peak fraction (peak A, B, and C) purified from cells co-expressing SC (A1+L+J+SC or A2m2+L+J+SC). (C, D, E) High-mass MALDI-TOF MS analysis of the each peak fraction containing recombinant IgA1 purified from the culture supernatant of cells transfected with A1, L, J, and SC. (C) One main peak (arrow) corresponding to monomer (Mo) was detected in the peak A fraction. (D) Two main peaks (arrows) corresponding to a dimer (Di) and a di-cation dimer (Di2+) were detected in the peak B fraction. (E) Three main peaks (arrows) corresponding to a tetramer (Te), trimer (Tr), and di-cation tetramer (Te2+) were detected in the peak C fraction. (F, G) High-mass MALDI-TOF MS analysis of the each peak fraction of recombinant IgA2m2 purified from the culture supernatant from cells transfected with A2m2, L, J, and SC. (F) One main peak (arrow) corresponding to a monomer (Mo) was detected in the peak A fraction. (G) Three main peaks (arrows) corresponding to a tetramer (Te), a trimer (Tr), and a di-cation tetramer (Te2+) were detected in the peak C fraction. (H) Quantification of the amount of each subunit within the peak B or C fraction of recombinant SIgA1 or SIgA2m2 antibodies purified from the culture supernatant of cells transfected with A1/L/J,/SC or A2m2/L/J/SC using LC-MS with stable isotope-labeled standard peptides. The abundance of each subunit to that of J chain is expressed as a ratio. Data are expressed as box-and-whisker plot with minimum, maximum, median, upper and lower quartiles (n = 6–7). (I) HS-AFM image of peak C derived from a recombinant SIgA1 (A1Te) or SIgA2m2 (A2m2Te) antibody purified from the culture supernatant of cells transfected with A1/L/J/SC or A2m2/L/J/SC. Scale bar, 20 nm.

*Shinji Saito , Kaori Sano , Tadaki Suzuki , Akira Ainai, Yuki Taga,  Tomonori Ueno, Koshiro Tabata, Kumpei Saito, Yuji Wada, Yuki Ohara, Haruko Takeyama, Takato Odagiri, Tsutomu Kageyama, Kiyoko Ogawa-Goto, Pretty Multihartina, Vivi Setiawaty, Krisna Nur Andriana Pangesti, Hideki Hasegawa
IgA tetramerization improves target breadth but not peak potency of functionality of anti-influenza virus broadly neutralizing antibody
PLoS Pathog 15(1): e1007427.
DOI: https://doi.org/10.1371/journal.ppat.1007427

Please follow this external link for the full article: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007427

Open Access: The article « IgA tetramerization improves target breadth but not peak potency of functionality of anti-influenza virus broadly neutralizing antibody » by Saito S, Sano K, Suzuki T, Ainai A, Taga Y, Ueno T, et al. (2019) 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/.