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150 results for “amyloid beta”
The effects of PaPE-1 on amyloid beta-induced neurotoxicity
<p>Data related to the article Posttreatment with PaPE-1 Protects from Aβ-Induced Neurodegeneration Through Inhibiting the Expression of Alzheimer's Disease-Related Genes and Apoptosis Process That Involves Enhanced DNA Methylation of Specific Genes. These are biochemical, molecular and microscopic data. We aimed to verify the neuroprotective capacity of PaPE-1 against amyloid beta (Aβ)-induced toxicity. Fig 1 – the presence of amyloid beta in cellular cultures; Fig 2 – the effects of apoptosis inhibitors on amyloid beta-induced caspase-3 activity; Fig 3 – the effects of amyloid beta and PaPE-1 on caspase -3, -8, and -9 activities; Fig 4 – effects of amyloid beta and PaPE-1 on Calcein AM and Hoechst 33342 staining; Fig 5 – effects of amyloid beta and PaPE-1 on expression of apoptosis related factors; Fig 6 – effects of amyloid beta and PaPE-1 on methylation of specific genes; Fig 7 – effects of amyloid beta and PaPE-1 on the degree of neurodegeneration; Fig 8 - effects of amyloid beta and PaPE-1 on the membrane stain; Fig 9 - effects of amyloid beta and PaPE-1 on the expression of Alzheimer’s disease-related genes.</p>
Supplemental data for: A bibliometric assessment of the incidence of amyloid-Eszett (Aß), a false positive of amyloid-beta (Aβ), in the neurodegenerative disease literature
<p>One claimed reason for the development of Alzheimer’s disease (AD), a prominent neurodegenerative disease, is the extracellular aggregation of amyloid-beta (Aβ). A linguistic or formatting error has resulted in the misrepresentation of the Greek letter β with the German letter Eszett (ß), resulting in the formation of a non-existent compound, amyloid-Eszett (Aß). These datasets offer a quantified appreciation of the AD-related literature, carrying a mention of this false positive in the title, abstract and keywords of papers indexed in the Web of Science Core Collection and Scopus. Also, as a curiosity given the popularity of this large language model, we asked the questions to ChatGPT. This AI chatbot developed by OpenAI was able to recognize Eszett as a linguistic or typographic error, within this context, recognizing Aß and Aβ as equals. This erroneous substitution of a Greek letter (in Aβ) by a German one (Aß), despite giving a non-existent compound, will likely not change the underlying scientific conclusions of the affected papers, although errata might be useful to enlighten others, including metadata managers and journal copyeditors, so as not to repeat the same mistake.</p>
Dataset for the Amyloid-beta precursor protein antibody screening study
<p>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Amyloid-beta precursor protein. The study is available on Zenodo (https://doi.org/10.5281/zenodo.7971926).</p>
Transcranial detection of amyloid-beta at single plaque resolution in vivo with large-field multifocal illumination fluorescence microscopy
<p>The abnormal deposition of beta-amyloid proteins in the brain is one of the major histopathological hallmarks of Alzheimer’s disease. Currently available intravital microscopy techniques can visualize plaques with high resolution, but are limited to a small field-of-view and with depth limitation. Here, we report the transcranial detection of amyloid-beta deposits at the whole brain scale with 20 mm resolution in APP/PS1 and arcAb mouse models of Alzheimer’s disease amyloidosis using a novel large-field multifocal illumination (LMI) fluorescence microscopy technique. High sensitive and specific detection of amyloid-beta deposits at single plaque level in APP/PS1 and arcAb mice was facilitated using luminescent conjugated oligothiophene HS-169. Immunohistochemical staining with HS-169, anti-Ab antibody 6E10, conformation antibodies OC (fibrillar) on brain tissue sections further showed that HS-169 resolved compact parenchymal and vessel-associated amyloid deposits. In conclusion, we demonstrate a new <em>in vivo </em>imaging platform for detection of amyloid-beta deposits at single plaque resolution in murine models of Alzheimer’s disease amyloidosis.</p>
Choline acetyltransferase (ChAT) - Amyloid beta peptides complex Molecular dynamics Trajectories
<p>In silico molecular dynamics study was performed for the choline acetyltransferase (ChAT) - Abeta peptides complex. The molecular docking of Aβ<sub>40 </sub>and Aβ<sub>42</sub> on ChAT suggested three most probable binding clusters for both the Aβ peptides. Thus generating ChAT-Aβ<sub>40</sub> Cluster-0, ChAT-Aβ<sub>40</sub> Cluster-1, ChAT-Aβ<sub>40</sub> Cluster-2 for Aβ<sub>40</sub> peptide on ChAT, likewise ChAT-Aβ<sub>42</sub> Cluster-0, ChAT-Aβ<sub>42</sub> Cluster-1, ChAT-Aβ<sub>42</sub> Cluster-2 were generated for Aβ<sub>42</sub> peptide on ChAT.</p> <p>Each of the folders contains the topology file with a ‘.gro’ extension and a trajectory file with ‘.xtc’ extension generated from the 100 ns molecular dynamics performed for each of the clusters mentioned above that were generated from the molecular docking. The folders are named as follows:</p> <ol> <li>ChAT_AB40_Cluster_0: Containing the topology file (ab40_0.gro) and the trajectory file (ab40_0.xtc)</li> <li>ChAT_AB40_Cluster_1: Containing the topology file (ab40_1.gro) and the trajectory file (ab40_1.xtc)</li> <li>ChAT_AB40_Cluster_2: Containing the topology file (ab40_2.gro) and the trajectory file (ab40_2.xtc)</li> <li>ChAT_AB42_Cluster_0: Containing the topology file (ab42_0.gro) and the trajectory file (ab42_0.xtc)</li> <li>ChAT_AB42_Cluster_1: Containing the topology file (ab42_1.gro) and the trajectory file (ab42_1.xtc)</li> <li>ChAT_AB42_Cluster_2: Containing the topology file (ab42_2.gro) and the trajectory file (ab42_2.xtc</li> </ol>
Amyloid-beta 16-22 peptide monomer simulation with the CHARMM-Drude force field and OpenMM (Run 1)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. This is the first independent simulation runs out of 3.</p> <p>Part 1-2 are 200 ns long, 3-8 are 100 ns each. Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>The system contains ~ 150 mM NaCl.</p>
Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the third out of three independent runs. </p> <p>Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>"</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3</p> <p>Total simulation time is 500 ns. Frames are saved with 100 ps frequency. </p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 2)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the second out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the third out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 1)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the first out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Data for: Sticker-and-Spacer Model for Amyloid Beta Condensation and Fibrillation
<p>Data for: Sticker-and-Spacer Model for Amyloid Beta Condensation and Fibrillation</p> <p>Preprint of the paper on bioRxiv:</p> <p>https://www.biorxiv.org/content/10.1101/2022.06.04.494837v1</p>
Figure 6 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 6. Treatment Group with resveratrol standard after induced by Beta-Amyloid (10 x10).
Figure 3 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 3. Treatment group: 2- ME + Resveratrol isolated from Tempeh (10 x10).
Figure 8 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 8. Treatment Group with resveratrol tempeh + 2-ME after induced by Beta-Amyloid (10 x10).
Figure 5 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 5. Treatment group: 2- ME (10 x10).
Figure 9. Treatment Group with 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 9. Treatment Group with 2-ME after induced by Beta-Amyloid (10 x10).
Figure 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 2. Treatment group: 2- ME + Resveratrol Standard (10 x10).
Figure 1 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 1. Control Group (10 x10).
Table 4 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol
<p><b>Table 4.</b> Cytotoxic effect of various concentrations of Resveratrol and 2-Methoxyethanol Against Primary Neuron cell viability in MTT assay (570 nm).</p><table><tbody><tr><th><b>% Inhibition</b></th></tr></tbody><tbody><tr><th><b>Concentration of 2-Methoxyethanol</b></th><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td></tr><tr><th><b>and Resveratrol</b></th><td><b>Resveratrol (Standard)</b></td><td><b>Resveratrol (Tempeh)</b></td><td><b>Resveratrol (Soybean Seed Coat)</b></td></tr><tr><th>IC50</th><td>(17.38 ± 0.99 µg/mL)</td><td>(31.14 ± 0.02 µg/mL)</td><td>(13.40 ± 0.30 µg/mL)</td></tr><tr><th>1.4 (µg/mL)</th><td>12.57</td><td>0</td><td>11.98</td></tr><tr><th>2.8 (µg/mL)</th><td>4.59</td><td>1.75</td><td>17.03</td></tr><tr><th>4.2 (µg/mL)</th><td>0</td><td>0</td><td>0</td></tr></tbody></table>
Table 3 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol
<p><b>Table 3.</b> Cytotoxic effect of various concentrations of Resveratrol and 2-Methoxyethanol Against Primary Neuron cell viability in MTT assay (540 nm).</p><table><tbody><tr><th><b>% Inhibition</b></th></tr></tbody><tbody><tr><th><b>Concentration of 2-Methoxyethanol</b></th><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td></tr><tr><th><b>and Resveratrol</b></th><td><b>Resveratrol (Standard)</b></td><td><b>Resveratrol (Tempeh)</b></td><td><b>Resveratrol (Soybean Seed Coat)</b></td></tr><tr><th>IC50</th><td>(17.64 ± 0.99 µg/mL)</td><td>(32.22 ± 1.18 µg/mL)</td><td>(17.43 ± 0.16 µg/mL)</td></tr><tr><th>1.4 (µg/mL)</th><td>11.8</td><td>0</td><td>7.95</td></tr><tr><th>2.8 (µg/mL)</th><td>5.27</td><td>0</td><td>14.41</td></tr><tr><th>4.2 (µg/mL)</th><td>0</td><td>0</td><td>0</td></tr></tbody></table>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.