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934 results for “Amino acids”
Parkin regulates amino acid homeostasis at mitochondria-lysosome (M/L) contact sites in Parkinson's disease
<p>Mutations in the E3 ubiquitin ligase parkin are the most common cause of early-onset Parkinson's disease (PD). Although parkin modulates mitochondrial and endolysosomal homeostasis during cellular stress, whether parkin regulates mitochondrial and lysosomal crosstalk under physiologic conditions remains unresolved. Using transcriptomics, metabolomics, and super-resolution microscopy, we identify amino acid metabolism as a disrupted pathway in iPSC-derived dopaminergic neurons from parkin PD patients. Compared to isogenic controls, parkin mutant neurons exhibit decreased mitochondria-lysosome contacts via destabilization of active Rab7. Subcellular metabolomics in parkin mutant neurons reveals amino acid accumulation in lysosomes and their deficiency in mitochondria. Knockdown of the Rab7 GTPase-activating protein TBC1D15 restores mitochondria-lysosome tethering and ameliorates cellular and subcellular amino acid profiles in parkin mutant neurons. Our data thus uncover a function of parkin in promoting mitochondrial and lysosomal amino acid homeostasis through stabilization of mitochondria-lysosome contacts and suggest that modulation of inter-organelle contacts may serve as a potential target for ameliorating amino acid dyshomeostasis in disease.</p>
Revisiting the HO●-initiated oxidation of L-proline amino acid in the aqueous phase – Influence of transition metal ions
<p>The oxidation of L-proline (Pro) by HO<sup>●</sup> radical in water and the influence of transition metal ions on this process has been revisited by using the density functional theory (DFT) method at the M05-2X/6-311++G(3df,3pd)//M05-2X/6-311++G(d,p) level of theory at the temperature of 298.15 K. HO<sup>●</sup>-initiated oxidation of Pro via hydrogen atom transfer (HAT) reactions is more favourable at the b- and g-carbon than at the a- and d-carbon. The total branching ratios are 44.6% and 39.5% for the β- and γ-carbon and 11.5% and 4.2% for the a- and d-carbon, respectively. The overall rate constant at 298.15 K is 6.04 × 10<sup>8</sup> M<sup>-1</sup> s<sup>-1</sup>. In addition, Pro tends to form the stable mono- and bi-dentate complexes with both Fe and Cu ions via the –COO functional group of dipole-salt form. The most stable Cu(II)-Pro complexes have high potential oxidant risks by enhancing the HO<sup>●</sup> radical formation in the presence of reducing agents such as superoxide anion or ascorbate anion. Besides, the complexes of the metal at a high oxidation state, i.e., Fe(III)-Pro and Cu(II)-Pro, show their ability to be oxidized by HO<sup>●</sup> radical via HAT reactions but with a lower rate constant than that of free Pro. Unsurprisingly, the oxidation enhancement is insignificant for SET reactions with almost negligible rate constants. In contrast, the rate constants of SET reactions of low oxidation state complexes (i.e., Fe(II)-Pro and Cu(I)-Pro) are faster than the oxidation rate of free ligands, and thus, these complexes promote the oxidation of Pro.</p>
Effects of proline on survival, locomotion, and amino acid haemolymph composition of Osmia cornuta (Latreille, 1805)
<p>This repository contains data of survival, feed intake, behaviour and concentration of haemolymph amino acids of mason bees (<em>Osmia cornuta</em> Latreille) fed artificial diets made of sucrose only (control group) or sucrose solution enriched with 10mM proline (proline group). </p>
gapseq reconstruction for 36 human gut bacterial strains with known amino acid auxotrophy status
<p>The data set contains genome-scale metabolic network reconstructions for 36 bacterial genomes, for which the auxotrophy/prototrophy status for amino acids has been reported in scientific literature based on laboratory experiments. Auxotrophy/Prototrophy information and the respective PubMed-IDs (PMID) are summarized in "Validation_models_Metadata.csv". Network reconstructions were made using gapseq (development version: 1.2 commit 2dfa8c80 ; Sequence DB md5sum: bf8ba98 (2023-02-15, Bacteria).</p> <p>The models were reconstructed using the following workflow.</p> <pre><code># Reaction & Pathway prediction ./gapseq find -b 200 -v 1 -p all -k -t Bacteria <genomeID>.fna.gz # Transporter prediction ./gapseq find-transport -b 200 -k <genomeID>.fna.gz # Draft network reconstruction ./gapseq draft -r <genomeID>-all-Reactions.tbl -t <genomeID>-Transporter.tbl -b Bacteria -c <genomeID>.fna.gz -p <genomeID>-all-Pathways.tbl -u 200 -l 100 # gapfill/growth medium prediction ./gapseq medium -m <genomeID>-draft.RDS -p <genomeID>-all-Pathways.tbl -c "cpd00007:0" # Gap-filling # (If H2 is part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100 -e highH2 # (If H2 is not part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100</code></pre> <p> </p>
A computational insight on the aromatic amino acids conjugation with [Cp*Rh(H2O)3]2+ by using the MTD/FMO3 approach.
<p>The zip file contains the 3D coordinates of the optimized structures, obtained by sampling each 1 ps of the EC1, EC2 and EC3 trajectories (MTD and MD calculations) and used as input geometries for FMO3 calculations.</p>
Supplementary Data to: "Organic Phases in Bivalve (Arctica islandica) Shells: Their Bulk and Amino Acid Nitrogen Stable Isotope Compositions" in Geochemistry, Geophysics, Geosystems
<p>This dataset contains the data generated for publication "Organic Phases in Bivalve (<em>Arctica islandica</em>) Shells: Their Bulk and Amino Acid Nitrogen Stable Isotope Compositions", including the following files:</p> <p>Specimen_ID_shell_morphology_measurement: Description of locality of collection, shell ID, shell working ID and the shell morphology measurement which can be referred to Section 2.1 of the manuscript.</p> <p>EA_IRMS_raw_error_propagate: This file contains data showing the m/z 28 signal intensities of all measurements and the error propagation that mentioned in Section 2.3 of the manuscript. It also includes the calculation of analytical accuracy and precision. </p> <p>Statistics: The file contains the summary of statistical analyses performed in this manuscript. Refer to Section 2.7 and 3.3.</p> <p>Recovery: It contains the recovery of the total nitrogen contents or amino acid concentrations after different treatments and this was mentioned in Section 4.1 of the manucript.</p> <p>Mass_balance: The computation procedure that showed in Section 3.4 and discussed in Section 4.3 can be traced in this file.</p> <p>GC-C-IRMS_long_term_sd: The file shows the long-term precision of GC-C-IRMS computed from the mixed standard of amino acids </p> <p>BSIA_d15N: The file contains all the bulk d15N data that used in this manuscript.</p> <p>CSIA_d15N: The file contains all the amino acid d15N data that used in this manuscript.</p> <p>AA_Composition: The file shows AA percent data that used in this manuscript.</p> <p><br> For details see main text of the manuscript.</p> <p><br> </p>
Study to Assess Hypoallergenicity of a New Amino-acid Based Infant Formula in Children With Cow's Milk Allergy
ClinicalTrials.gov study NCT02414243. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Muscle Regrowth During Physical Rehabilitation and Amino Acid Supplementation
ClinicalTrials.gov study NCT00760383. IPD Sharing: Not stated. Countries: 1. Publications: 9.
Exploring the Effectiveness and Safety of Amino Acid Peritoneal Dialysis Solution
ClinicalTrials.gov study NCT06358820. IPD Sharing: NO. Countries: 1. Publications: 1.
Gamma-Amino Butyric Acid (GABA)-A Alpha2/3 Study
ClinicalTrials.gov study NCT00129441. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Phase 2 Study of Glycomacropeptide Versus Amino Acid Diet for Management of Phenylketonuria
ClinicalTrials.gov study NCT01428258. IPD Sharing: NO. Countries: 1. Publications: 13.
Amino Acids in Patients With Anorexia Nervosa: Double-blind Randomized Study Versus Placebo
ClinicalTrials.gov study NCT05290285. IPD Sharing: NO. Countries: 1. Publications: 6.
Sulfur Amino Acids, Energy Metabolism and Obesity
ClinicalTrials.gov study NCT04701346. IPD Sharing: NO. Countries: 1. Publications: 3.
Changes in Amino Acid Absorption After Adding a Probiotic to an Acute Protein Feeding
ClinicalTrials.gov study NCT04427020. IPD Sharing: NO. Countries: 1. Publications: 1.
Branched-chain Amino Acid Supplementation for Hepatocellular Carcinoma
ClinicalTrials.gov study NCT03908255. IPD Sharing: YES. Countries: 1. Publications: 7.
Single Low-Dose of Supplement Amino Acid
ClinicalTrials.gov study NCT01540773. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Amino Acid-based Oral Rehydration Solution in Children With Short Bowel Syndrome
ClinicalTrials.gov study NCT03105362. IPD Sharing: NO. Countries: 1. Publications: 22.
Essential Amino Acids and High Intensity Interval Training
ClinicalTrials.gov study NCT04080102. IPD Sharing: YES. Countries: 1. Publications: 1.
Perioperative Use of Amino Acids in Recipients of Orthotopic Liver Transplantation as a Renal Protective Factor
ClinicalTrials.gov study NCT07004387. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Pilot Phase I/II Study of Amino Acid Leucine in Treatment of Patients With Transfusion-Dependent Diamond Blackfan Anemia
ClinicalTrials.gov study NCT01362595. IPD Sharing: NO. Countries: 1. Publications: 50.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.