Tag: SPM probes

Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas

Dietary fibers have been shown to exert immune effects via interaction with pattern recognition receptors (PRR) such as toll-like receptors (TLR) and nucleotide-binding oligomerization domain (NOD)-like receptors. Pectin is a dietary fiber that interacts with PRR depending on its chemical structure. Papaya pectin retains different chemical structures at different ripening stages. How this influences PRR signalling is unknown.*

The aim of the article “Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas” by Samira B. R. Prado, Martin Beukema, Eva Jermendi, Henk A. Schols, Paul de Vos and João Paulo Fabi was to determine how ripening influences pectin structures and their ability to interact with TLR2, 3, 4, 5 and 9, and NOD1 and 2.*

Papaya ripening is an enzymatic, biochemically driven process that occurs over a short period of time (five days) and involves the mobilization of pectin and the alteration of its chemical composition.

The authors evaluated the interaction of the water-soluble fractions rich in pectin extracted from unripe to ripe papayas. The pectin extracted from ripe papayas activated all the TLR and, to a lesser extent, the NOD receptors. The pectin extracted from unripe papayas also activated TLR2, 4 and 5 but inhibited the activation of TLR3 and 9.*

During papaya ripening, profound changes in pectin structures lead to differences in the biological effects. The data presented in the paper show that papaya pectin extracted from fruit pulp at different ripening points differently interacted with PRR in a ripening-dependent way. The longer chains of HG from unripe papayas pectin, which were less methyl-esterified, inhibited the activation of TLR3 and 9 and activated TLR2 and 4, in contrast to the ripe papaya’s pectin, which have smaller HG chains with medium methyl esterification thus activating TLR2, 3, 4, 5 and 9.*

This variation may represent new biological features of papaya pectin structures in addition to anticancer activities, possibly creating new and cost-effective approaches to extracting papaya pectin with desirable structural and biological features.*

These findings might lead to selection of ripening stages for tailored modulation of PRR to support or attenuate immunity in consumers.*

The changes in Molecular weight ( Mw ) can also be visualized by Atomic Force Microscopy (see Fig. 1C in the paper.)

The AFM images presented in the paper were acquired in tapping mode using an NanoWorld Pointprobe® NCHR AFM probe with a typical spring constant of 42 N/m and typically 320 kHz resonance frequency. The scan speed and scanning resolution were 0.5 Hz and 512 × 512 points, respectively.*

Figure 1 C from “Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas” by Samira B. R. Prado et al. 2020:
(C) Representative topographical AFM images of Un-1-WSF and R-2-WSF. White arrow indicates linear structures, black arrow aggregates and grey arrow the smaller structure from the R-2-WSF. Un-1-WSF: unripe – papaya from 1st day after harvest – water-soluble fraction; Un-2-WSF: unripe – papaya from 2nd day after harvest – water-soluble fraction; I-WSF: intermediate ripening time point – papaya from 3rd day after harvest – water-soluble fraction; R-1-WSF: ripe – papaya from 4th day after harvest – water-soluble fraction; R-2-WSF: ripe – papaya from 5th day after harvest – water-soluble fraction. Please have a look at the full article for the full figure.

*Samira B. R. Prado, Martin Beukema, Eva Jermendi, Henk A. Schols, Paul de Vos and João Paulo Fabi
Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas
Nature Scientific Reports volume 10, Article number: 1690 (2020)
DOI: https://doi.org/10.1038/s41598-020-58311-0

Please follow this external link to read the full article https://rdcu.be/b3Fnb .

Open Access The article “ Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas “ by Samira B. R. Prado, Martin Beukema, Eva Jermendi, Henk A. Schols, Paul de Vos and João Paulo Fabi 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/.

Graphene Quantum Dots as Nanozymes for Electrochemical Sensing of Yersinia enterocolitica in Milk and Human Serum

Yersinia enterocolitica is a gram-negative bacillus shaped bacterium that leads to a zootonic disease called yersiniosis. The infection is demonstrated as mesenteric adenitis, acute diarrhea, terminal ileitis, and pseudoappendicitis. Rarely, it can even result in sepsis. According to the 2017 report of the European Food Safety Authority (EFSA) and European Centre for Disease Prevention and Control (ECDC), Y. enterocolitica has been realized as the third most common foodborne-zoonotic disease after campylobacteriosis and salmonellosis in the European Union.*

Several studies suggested that the bacterium cannot survive after a proper pasteurization process, although contrary findings were also reported. The quick and accurate detection of the bacterium from food products or the body fluids of infected individuals is, therefore, important.*

Biosensors offer strong alternatives to the already existing detection techniques for rapid and sensitive quantification of Y. enterocolitica.*

In their paper “Graphene Quantum Dots as Nanozymes for Electrochemical Sensing of Yersinia enterocolitica in Milk and Human Serum” Sumeyra Savas and Zeynep Altintas describe a novel immunosensor approach using graphene quantum dots (GQDs) as enzyme mimics in an electrochemical sensor set up to provide an efficient diagnostic method for Y. enterecolitica.*

The developed method can be used for any pathogenic bacteria detection for clinical and food samples without pre-sample treatment. Offering a very rapid, specific and sensitive detection with a label-free system, the GQD-based immunosensor can be coupled with many electrochemical biosensors.*

The bare gold, GQD-laminated, and antibody-immobilized sensor surfaces were characterized by atomic force microscopy (AFM) using NanoWorld Pointprobe® NCLR AFM probes.*

Figure 4 from “Graphene Quantum Dots as Nanozymes for Electrochemical Sensing of Yersinia enterocolitica in Milk and Human Serum“ by S. Savas and Z. Altintas:
AFM analysis of bare (A), GQD-laminated (B), and antibody-immobilized (C) sensor surfaces.

*Sumeyra Savas and Zeynep Altintas
Graphene Quantum Dots as Nanozymes for Electrochemical Sensing of Yersinia enterocolitica in Milk and Human Serum
Materials 2019, 12(13), 2189
DOI: https://doi.org/10.3390/ma12132189

Please follow this external link to read the full article: https://www.mdpi.com/1996-1944/12/13/2189

Open Access The article “Graphene Quantum Dots as Nanozymes for Electrochemical Sensing of Yersinia enterocolitica in Milk and Human Serum “ by Sumeyra Savas and Zeynep Altintas 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/.

The free energy landscape of retroviral integration

Retroviral integration, the process of covalently inserting viral DNA into the host genome, is a point of no return in the replication cycle. Yet, strand transfer is intrinsically iso-energetic and it is not clear how efficient integration can be achieved.*

In the article “The free energy landscape of retroviral integration” published in Nature Communications Willem Vanderlinden, Tine Brouns, Philipp U. Walker, Pauline J. Kolbeck, Lukas F. Milles, Wolfgang Ott, Philipp C. Nickels, Zeger Debyser and Jan Lipfert use biochemical assays, atomic force microscopy (AFM), and multiplexed single-molecule magnetic tweezers (MT) to study tetrameric prototype foamy virus (PFV) strand-transfer dynamics.*

Their finding that PFV intasomes employ auxiliary-binding sites for modulating the barriers to integration raises the question how the topology of higher-order intasomes governs integration of pathogenic retroviruses, most notably HIV. The single-molecule assays developed in this work are expected to be particularly useful to further unravel the complexity of this important class of molecular machines.*

The AFM images were recorded in amplitude modulation mode under ambient conditions and by using NanoWorld high resolution SuperSharpSilicon™ SSS-NCH cantilevers ( resonance frequency ≈300 kHz; typical end-radius 2 nm; half-cone angle <10 deg). Typical scans were recorded at 1–3 Hz line frequency, with optimized feedback parameters and at 512 × 512 pixels.*

Figure 2 e, f and g from “The free energy landscape of retroviral integration” by Willem Vanderlinden et al. (please refer to the full article for the complete figure 2 https://rdcu.be/b0R63 ) : e Atomic Force Microscopy image of intasomes incubated briefly (2 min) with supercoiled plasmid DNA, depicting a branched complex as found in ~50% of early complexes. f Atomic Force Microscopy image of a bridging complex that dominates (~80%) the population of complexes at longer (>45 min) incubation. g Atomic Force Microscopy image of a gel-purified STC
Figure 2 e, f and g from “The free energy landscape of retroviral integration” by Willem Vanderlinden et al.
(please refer to the full article for the complete figure 2 https://rdcu.be/b0R63 ) :
 e AFM image of intasomes incubated briefly (2 min) with supercoiled plasmid DNA, depicting a branched complex as found in ~50% of early complexes.
 f AFM image of a bridging complex that dominates (~80%) the population of complexes at longer (>45 min) incubation.
g AFM image of a gel-purified STC

*Willem Vanderlinden, Tine Brouns, Philipp U. Walker, Pauline J. Kolbeck, Lukas F. Milles, Wolfgang Ott, Philipp C. Nickels, Zeger Debyser, Jan Lipfert
The free energy landscape of retroviral integration
Nature Communications volume 10, Article number: 4738 (2019)
DOI: https://doi.org/10.1038/s41467-019-12649-w

Please follow this external link to read the full article: https://rdcu.be/b0R63

Open Access The article “The free energy landscape of retroviral integration“ by Willem Vanderlinden, Tine Brouns, Philipp U. Walker, Pauline J. Kolbeck, Lukas F. Milles, Wolfgang Ott, Philipp C. Nickels, Zeger Debyser and Jan Lipfert 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/.