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29 results for “functional amyloid”
III PhasAGE International Conference - Design of novel functional amyloid assemblies - Lecture
<p>The III PhasAGE International Conference "Multiscale understanding of protein aggregation and biomolecular condensates in aging and disease" brought together members of the PhasAGE consortium as well as outstanding international speakers from multidisciplinary fields dedicated to unraveling the intricacies of protein aggregation and biomolecular condensates in the context of aging and disease. For details on the conference program please see https://phasage.eu/iii-phasage-international-conference/. </p>
Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids - Datasets
<p>This repository contains data from work "Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids"<br><br></p> <p><a href="https://zenodo.org/api/records/14016809/draft/files/BFA.fasta/content" target="_blank" rel="noopener noreferrer">BFA.fasta</a> - fasta file containing sequences of bacterial functional amyloids used as a query for identification of novel bacterial functional amyloids in UHGP dataset</p> <p><a href="https://zenodo.org/api/records/14016809/draft/files/UHGPAmyloids.fasta/content" target="_blank" rel="noopener noreferrer">UHGPAmyloids.fasta </a>- fasta file containing sequences of amyloids identified in UHGP dataset</p> <p><a href="https://zenodo.org/api/records/14016809/draft/files/UHGPAmyloids.csv/content" target="_blank" rel="noopener noreferrer">UHGPAmyloids.csv</a> - csv file containing information about amyloids identified in UHGP</p> <p>Columns:<br>query_id - Uniprot id of the protein from BFA<br>query_gene_name - gene name of the protein from BFA<br>target_id - UHGP id of the found homolog<br>ProbabilityAMYPred-FRL - score obtained for the target_id sequence according to AMYPred-FRL<br>Archcandy - Prediction of beta arch motif for identified amyloid<br>Genome - UHGP genome id of the target_id<br>Localization - predicted subcellular localization with BUSCA for target_id sequence<br>Lineage - full taxonomy of the target_id sequence (which bacteria produced this specific sequence) </p> <p><a href="https://zenodo.org/api/records/14016809/draft/files/PPIPositivePredictionsBetween_UHGPAmyloids_And_HPAIntestine_filtered.csv/content" target="_blank" rel="noopener noreferrer">PPIPositivePredictionsBetween_UHGPAmyloids_And_HPAIntestine_filtered.csv</a> - csv file contining inforamtions about predicted protein-protein interactions between UHGPAmyloids and human proteins expressed in guts</p> <p>Columns:<br>UHGPAmyloids_id - UHGPAmyloids id (same as target_id in UHGPAmyloids.csv)<br>hp_uniprot_name - Uniprot name of a human protein<br>negative and score - scores returned by ProteinPrompt softwawre for prediction of PPI<br>hp_uniprot_id - Uniprot id of a human protein<br>BFA_sp_uniprot_id - Uniprot id of a BFA source protein<br>BFA_sp_uniprot_name - gene name of a BFA source protein<br>UHGPAmyloids_localization - predicted subcellular localization with BUSCA for UHGPAmyloids_id sequence<br>UHGPAmyloids_lineage - full taxonomy of the UHGPAmyloids_id sequence (which bacteria produced this specific sequence) </p>
Data from: The presubiculum links incipient amyloid and tau pathology to memory function in older persons
Objective: To identify the hippocampal subregions linking initial amyloid and tau pathology to memory performance in clinically normal older individuals, reflecting preclinical Alzheimer's disease (AD). Methods: A total of 127 individuals from the Harvard Aging Brain Study (Mean age: 76.22 years ± 6.42, 68 females (53.5%)) with a Clinical Dementia Rating score of 0, a flortaucipir tau-PET scan, a Pittsburgh Compound B amyloid-PET scan, a structural MRI scan and cognitive testing were included. From these images, we calculated neocortical, hippocampal and entorhinal amyloid pathology, entorhinal and hippocampal tau pathology and the volumes of six hippocampal subregions and total hippocampal volume. Memory was assessed with the selective reminding test. Mediation and moderation analyses modeled associations between regional markers and memory. Analyses included covariates for age, sex and education. Results: Neocortical amyloid, entorhinal tau and presubiculum volume univariately associated with memory performance. The relationship between neocortical amyloid and memory was mediated by entorhinal tau and presubiculum volume, which was modified by hippocampal amyloid burden. With other biomarkers held constant, presubiculum volume was the only marker predicting memory performance in the total sample and in individuals with elevated hippocampal amyloid burden. Conclusions: The presubiculum captures unique AD-related biological variation that is not reflected in total hippocampal volume. Presubiculum volume may be a promising marker of imminent memory problems, and can contribute to understanding the interaction between incipient AD-related pathologies and memory performance. The modulation by hippocampal amyloid suggests that amyloid is a necessary process – but not sufficient – to drive neurodegeneration in memory-related regions.
Remediation of Metal Oxide Nanotoxicity with A Functional Amyloid
<p>The molecular dynamics simulations on the binding of metal ions with the beta-lactoglobulin (bLg) amyloid fibrils.</p>
Data from: The presubiculum links incipient amyloid and tau pathology to memory function in older persons
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Cognitive Function and Prevalence of Amyloid Marker in Frail Older Adults
ClinicalTrials.gov study NCT03129269. IPD Sharing: NO. Countries: 1. Publications: 10.
Data from: Amyloid and cerebrovascular burden divergently influence brain functional network changes over time
Objective: To examine the effects of baseline Alzheimer's disease and cerebrovascular disease markers on longitudinal default mode network (DMN) and executive control network (ECN) functional connectivity (FC) changes in mild cognitive impairment (MCI) patients. Methods: We studied 30 amnestic (aMCI) and 55 subcortical vascular MCI (svMCI) patients with baseline Pittsburgh Compound B (PiB)–positron emission tomography (PET) scans and longitudinal magnetic resonance imaging (MRI) scans. Participants were followed up clinically with annual MR imaging for up to four years (aMCI: 26 with two time-points, 4 with three time-points; svMCI: 13 with two time-points, 16 with three time-points, 26 with four time-points). Results: Amyloid-β burden was associated with longitudinal DMN FC declines, while cerebrovascular burden was associated with longitudinal ECN FC changes. When patients were divided into PiB+ and PiB- groups, PiB+ patients showed longitudinal DMN FC declines, while svMCI patients showed longitudinal ECN FC increases. Direct comparisons between the two groups without mixed pathology (aMCI PiB+ and svMCI PiB-) recapitulated this divergent pattern: aMCI PiB+ patients showed steeper longitudinal DMN FC declines, while svMCI PiB- patients showed steeper longitudinal ECN FC increases. Finally, using baseline PiB uptake and lacune numbers as continuous variables, baseline PiB uptake showed inverse U-shape associations with longitudinal DMN FC changes in both MCI subtypes, while baseline lacune numbers showed both mainly inverse-U shape relationships with longitudinal ECN FC changes in svMCI patients. Conclusions: Our findings underscore the divergent effects of amyloid-β and cerebrovascular burden on longitudinal FC changes in the DMN and ECN in the pre-dementia stage, which reflect the underlying pathology and may be used to track early changes in Alzheimer's disease and cerebrovascular disease.
Data from: Functional amyloids promote retention of public goods in bacteria
The growth and virulence of bacteria depends upon a number of factors that are secreted into the environment. These factors can diffuse away from the producing cells, to be either lost or utilized by cells that do not produce them (cheats). Mechanisms that act to reduce the loss of secreted factors through diffusion are expected to be favoured. One such mechanism may be the production of Fap fibrils, needle-like fibres on the cell surface observed in P.aeruginosa, which can transiently bind several secreted metabolites produced by cells. We test whether Fap fibrils help retain a secreted factor, the iron-scavenging molecule pyoverdine, and hence reduce the potential for exploitation by non-producing, cheating cells. We found that: (1) wildtype cells retain more iron-chelating metabolites than fibril non-producers; (2) purified Fap fibrils can prevent the loss of the iron-chelators PQS (Pseudomonas quinolone signal) and pyoverdine; and (3) pyoverdine non-producers have higher fitness in competition with fibril non-producers than with wildtype cells. Our results suggest that by limiting the loss of a costly public good, Fap fibrils may play an important role in stabilizing cooperative production of secreted factors.
Data from: Amyloid and cerebrovascular burden divergently influence brain functional network changes over time
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Data from: Functional amyloids promote retention of public goods in bacteria
Open the record for dataset details and reuse information.
Immunotherapy against amyloid beta is modulated by meningeal lymphatic function II
GEO Series GSE141872. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Early Modulation of the Gut Microbiome by Female Sex Hormones Alters Amyloid Pathology and Microglial Function
GEO Series GSE245831. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Immunotherapy against amyloid beta is modulated by meningeal lymphatic function III
GEO Series GSE141915. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Functional TDP-43 amyloids bind sarcomeric mRNA to direct skeletal muscle formation
GEO Series GSE104796. Mus musculus. 8 samples. Type: Other.
Transcriptional, behavioural and biochemical profiling in the 3xTg-AD mouse model reveals a specific signature of amyloid deposition and functional decline in Alzheimer’s disease
GEO Series GSE161904. Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing.
Immunotherapy against amyloid beta is modulated by meningeal lymphatic function I
GEO Series GSE141849. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Endothelial Cell Senescence Stimulates Amyloid-β Phagocytosis and Barrier Function of Microglia Leading to Attenuation of Cognitive Impairment in the APPswe/PS1dE9 Mouse Model of Alzheimer’s Disease
GEO Series GSE223394. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Dual functionality of the TasA amyloid protein in Bacillus physiology and fitness on the phylloplane
GEO Series GSE124307. Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10. 12 samples. Type: Expression profiling by high throughput sequencing.
Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function
GEO Series GSE161952. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Amyloid beta 42 alters cardiac metabolism and impairs cardiac function in obesity
GEO Series GSE213708. Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing.
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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.