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934 results for “Amino acids”
Amino acid variation in HLA class II proteins is a major determinant of humoral response to common viruses - GWAS summary results
<p>Online Supplementary Dataset of the manuscript "Amino acid variation in HLA class II proteins is a major determinant of humoral response to common viruses": http://www.cell.com/ajhg/fulltext/S0002-9297(15)00372-9</p>
Influence of Volatile Anesthesia on the Release of Glutamate and other Amino Acids in the Nucleus Accumbens of Alcohol-Withdrawn Rats
<p>An alcohol withdrawal syndrome is a potentially life-threatening condition, which may occur when patients with alcohol use disorders have to undergo general anesthesia. Excitatory amino acids, such as glutamate, act as neurotransmitters and play a key role in alcohol withdrawal. We investigated the influence of isoflurane, sevoflurane, and desflurane anesthesia on the profile of excitatory and inhibitory amino acids in the Nucleus accumbens (NAcc) of alcohol-withdrawn rats (AWR).</p> <p>80 Wistar rats were randomized into two groups of 40, pair-fed with alcoholic or non-alcoholic nutrition. Nutrition was withdrawn and microdialysis trials were performed to measure the activity of amino acids in the NAcc. The withdrawal onset time was determined in a first trial with 20 rats. 60 rats then received isoflurane, sevoflurane, or desflurane anesthesia for three hours during withdrawal period, followed by one hour of elimination. Amino acid concentrations were obtained by chromatography. Quantification was done by integration and analysis of the area under the curve (AUC).</p>
Influence of Volatile Anesthesia on the Release of Glutamate and other Amino Acids in the Nucleus Accumbens of Alcohol-Withdrawn Rats
<p>An alcohol withdrawal syndrome is a potentially life-threatening condition, which may occur when patients with alcohol use disorders have to undergo general anesthesia. Excitatory amino acids, such as glutamate, act as neurotransmitters and play a key role in alcohol withdrawal. We investigated the influence of isoflurane, sevoflurane, and desflurane anesthesia on the profile of excitatory and inhibitory amino acids in the Nucleus accumbens (NAcc) of alcohol-withdrawn rats (AWR).</p> <p>80 Wistar rats were randomized into two groups of 40, pair-fed with alcoholic or non-alcoholic nutrition. Nutrition was withdrawn and microdialysis trials were performed to measure the activity of amino acids in the NAcc. The withdrawal onset time was determined in a first trial with 20 rats. 60 rats then received isoflurane, sevoflurane, or desflurane anesthesia for three hours during withdrawal period, followed by one hour of elimination. Amino acid concentrations were obtained by chromatography. Quantification was done by integration and analysis of the area under the curve (AUC).</p>
Amino acid composition of human salivary proteins
<p>This file contains information about amino acid composition of 872 human salivary proteins</p>
Supplemental data for: Sex differences in branched-chain amino acid and tryptophan metabolism and pathogenesis of youth-onset type 2 diabetes
<p>Supplemental data for: Sex differences in branched-chain amino acid and tryptophan metabolism and pathogenesis of youth-onset type 2 diabetes. </p><p>Metabolites measured from spot urine samples of youth and adolescents. </p>
Fig. 2 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties
Fig. 2. Biplot of Principal Component Analysis based on VOCs and Amino acids from leaves of Solanum allotetraploids (a), autotetraploids (b) and cultivated varieties (c). Components were calculated using Euclidean distances. Amino acids are depicted in the three-letter code. a) Allotetraploids (4xAL2 and 4xAL4) and diploid S. tuberosum x S. kurtzianum parental interspecific hybrid (2xPIH). b) Autotetraploids (4xAuL1, 4xAuL2 and 4xAuL3) and diploid S. kurtzianum parental line (2xPL). c) S. tuberosum cultivated varieties (4xCalen, 4xInnovator and 4xPampeana).
Fig. 3 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties
Fig. 3. Hierarchical cluster analysis (represented by a heat-map) of amino acids content in leaves of potato allo- and autotetraploids and cultivated varieties. Dendrograms were constructed by UPGMA clustering method for 18 amino acids and 10 lines: diploid S. kurtzianum parental line (2xPL), diploid S. tuberosum x S. kurtzianum parental interspecific hybrid (2xPIH), three autotetraploids (4xAuL1, 4xAuL2 and 4xAuL3), two allotetraploids (4xAL2 and 4xAL4) and three cultivated varieties (4xCalen, 4xInnovator and 4xPampeana).
Fig. 1 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties
Fig. 1. Fold change of compounds content in allotetraploids (a) and autotetraploids (b) relative to their respective diploid parental line. Fold change is expressed as log10(Tetraploid/Diploid). Horizontal lines are the average of the absolute logFC for each evaluated line, letters denote differences by Duncan's multiple range test (P <0.05).
Data for: Torii et al., Influence of amino acid substitutions in capsid proteins of coxsackievirus B5 on free chlorine and thermal inactivation
<p>This folder contains the experimental data for the figures shown in the main manuscript.</p>
Raw data for the article "Interrupted Polonovski strategy for the synthesis of functionalized amino acids and peptides"
<p>Raw NMR, IR, and MS data for the article "Interrupted Polonovski strategy for the synthesis of functionalized amino acids and peptides" published in Organic Letters, DOI: </p> <p><a title="DOI URL" href="https://doi.org/10.1021/acs.orglett.3c03603">https://doi.org/10.1021/acs.orglett.3c03603</a></p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.</p>
Data from: The twenty amino acids are identified by unique numbers assigned to the uracil, cytosine, adenine, and guanine found in the three base positions of the sixty-four messenger RNA genetic codons
<p>A codon's three bases consist of any combination of uracil, cytosine, adenine, or guanine and these encode the twenty amino acids. When the codon's first two bases are given specific values, and those values are multiplied, then the third base of the codon is used during translation only when the product is greater than three. Here we show that those values plus more variables within the ribosomal decoding site results in specific flow values for each of the twenty amino acid groups. These results are demonstrated in a flow chart showing the unidirectional flow which is expected during the translation process. All twenty amino acids can be represented by numbers that describe their relationship to each other and to the decoding site. We anticipate our findings will increase discussion about using a number system to better understand the translation process.</p>
Scripts for "In-Silico-Assisted Derivatization of Triarylboranes for the Catalytic Reductive Functionalization of Aniline-Derived Amino Acids and Peptides with H2"
<p>Please carefully read "README" file enclosed.</p>
Supplementary files for "Fast and sensitive quantification of AccQ-Tag derivatized amino acids and biogenic amines by UHPLC-UV from complex biological samples"
<p>Supplementary files for "Fast and sensitive quantification of AccQ-Tag derivatized amino acids and biogenic amines by UHPLC-MS from complex biological samples"</p>
Amino acid d13C dataset for nearshore marine primary producers
<p>Carbon isotope fingerprinting, or multivariate analysis using <em>δ</em><sup>13</sup>C values of individual compounds, is a powerful tool in ecological studies, particularly measurements of essential amino acids (EAA <em>δ</em><sup>13</sup>C). Despite the widespread application of this technique, there has been little methodological validation to determine (1) whether multivariate EAA <em>δ</em><sup>13</sup>C signatures (fingerprints) of primary producer groups vary across space and time, and (2) what biochemical mechanisms drive these patterns.</p> <p>Here, we evaluate the spatiotemporal consistency in EAA <em>δ</em><sup>13</sup>C fingerprints among nearshore primary producers: Chlorophyta (<em>Ulva</em> sp.), Ochrophyta (kelps), particulate organic matter (POM) and phytoplankton, and Rhodophyta. We analyzed 135 samples from 14 genera collected in Alaska, California, and Chile. The collections included historical museum samples (1896-1980 CE) of the giant kelp, <em>Macrocystis pyrifera</em>. We employed canonical analysis of principal coordinates and generalized linear models (GLMs) to respectively characterize isotopic fingerprints and evaluate the effect of taxonomy, local upwelling regimes, ecological setting, and time on individual EAA <em>δ</em><sup>13</sup>C values and associated fingerprints. We also calculated amino acid discrimination values (<em>D</em><sup>13</sup>C) to identify key biochemical pathways responsible for these patterns.</p> <p>We found remarkable consistency in EAA <em>δ</em><sup>13</sup>C fingerprints of marine algae across space and through time. Kelps and rhodophytes exhibited statistically distinct multivariate isotopic patterns regardless of geographic location, species identity, or time (kelps). In contrast, isotopic fingerprints of POM/phytoplankton and <em>Ulva</em> overlapped substantially. GLMs indicated that producer family, presumably due to the presence/absence of carbon concentrating mechanisms, and site locality are important determinants of individual amino acid <em>δ</em><sup>13</sup>C values. Taxonomy was also a key variable for EAA <em>δ</em><sup>13</sup>C fingerprints. The calculated discrimination values suggest variation in (1) metabolism of pyruvate and oxaloacetate-derived amino acids, and (2) production of storage and structural carbohydrates, are responsible for taxonomic differences in isotopic fingerprints. </p> <p>We conclude EAA <em>δ</em><sup>13</sup>C fingerprinting is a robust method for tracing the contribution of diverse primary producer taxa to coastal food webs. We show that this technique can be applied to modern and historical samples, as well as consumers collected across continental scales. The high fidelity of EAA <em>δ</em><sup>13</sup>C multivariate patterns coupled with biochemical mechanisms provides a powerful framework for future studies of carbon flow across broad biogeographical and ecological contexts.</p>
Recoding amino acids to a reduced alphabet may increase or decrease phylogenetic accuracy
<p>Common molecular phylogenetic characteristics such as long branches and compositional heterogeneity can be problematic for phylogenetic reconstruction when using amino acid data. Recoding alignments to reduced alphabets before phylogenetic analysis has often been used both to explore and potentially decrease the effect of such problems. We tested the effectiveness of this strategy on topological accuracy using simulated data on four-taxon trees. We simulated alignments in phylogenetically challenging ways to test the phylogenetic accuracy of analyses using various recoding strategies together with commonly-used homogeneous models. We tested three recoding methods based on amino acid exchangeability, and another recoding method based on lowering the compositional heterogeneity among alignment sequences as measured by the Chi-squared statistic. Our simulation results show that on trees with long branches where sequences approach saturation, accuracy was not greatly affected by exchangeability-based recoding, but Chi-squared-based recoding decreased accuracy. We then simulated sequences with different kinds of compositional heterogeneity over the tree. Recoding often increased accuracy on such alignments. Exchangeability-based recoding was rarely worse than not recoding, and often considerably better. Recoding based on lowering the Chi-squared value improved accuracy in some cases but not in others, suggesting that low compositional heterogeneity by itself is not sufficient to increase accuracy in the analysis of these alignments. We also simulated alignments using site-specific amino acid profiles, making sequences that had compositional heterogeneity over alignment sites. Exchangeability-based recoding coupled with site-homogeneous models had poor accuracy for these datasets but Chi-squared-based recoding on these alignments increased accuracy. We then simulated datasets that were compositionally both site- and tree-heterogeneous, like many real datasets. The effect on accuracy of recoding such doubly problematic datasets varied widely, depending on the type of compositional tree-heterogeneity and on the recoding scheme. Interestingly, analysis of unrecoded compositionally heterogeneous alignments with the NDCH or CAT models was generally more accurate than homogeneous analysis, whether recoded or not. Overall, our results suggest that making trees for recoded amino acid datasets can be useful, but they need to be interpreted cautiously as part of a more comprehensive analysis. The use of better fitting models like NDCH and CAT, which directly account for the patterns in the data, may offer a more promising long-term solution for analysing empirical data.</p>
Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models
<p><span>Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly-used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time non-reversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the non-reversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of datasets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the dataset. Notably, for the recently published plant and bird trees, these non-reversible models correctly recovered the commonly estimated root placements with very high statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (<a href="http://www.iqtree.org">http://www.iqtree.org</a>), allowing users to estimate non-reversible models and rooted phylogenies from their own protein datasets.</span></p>
Parthenogenesis doubles the rate of amino acid substitution in Whiptail mitochondria
<p class="MsoNormal"><span>Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the d<em>N</em>/d<em>S</em> ratios in asexual vertebrate lineages in the genus <em>Aspidoscelis</em> using whole mitochondrial genomes from seven asexual and five sexual species. We found higher d<em>N</em>/d<em>S</em> ratios in asexual <em>Aspidoscelis </em>species, indicating that asexual whiptails accumulate non-synonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provided empirical evidence to corroborate the connection between asexuality and increased </span><span>amino acid substitutions</span><span> in asexual vertebrate lineages.</span></p> <p class="MsoNormal"><span> </span></p>
Disruption of the TCA cycle reveals an ATF4-mediated integration of redox and amino acid metabolism
<p>The Tricarboxylic Acid (TCA) cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH), using an FH inhibitor (FHIN-1), and succinate dehydrogenase (SDH), using two inhibitors Atpenin A5 (AA5) and thenoyltrifluoroacetone (TTFA), and combined transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in murine kidney epithelial cell line.</p> <p>Data from this study that is included in this Dryad submission is as follows:</p> <p>1. TruSeq mRNA stranded analysis of murine Fh1<sup>fl/fl</sup> kidney epithelial cells were treated with vehicle control (DMSO) or 20 micromolar fumarate hydratase inhibitor (FHIN-1) for 24 h. Three biological replicates per condition. </p> <p>2. TruSeq mRNA stranded analysis of murine Fh1<sup>fl/fl</sup> kidney epithelial cells treated with vehicle control (DMSO) or Atpenin A5 (AA5) for 24 h. Three biological replicates per condition. </p> <p>3. Label-free proteomic analysis of a murine Fh1<sup>fl/fl</sup> kidney epithelial cells treated with vehicle control (DMSO) or 20 micromolar FHIN-1 for 24 h. Five biological replicates per condition. </p> <p>4. Label-free proteomic analysis of a murine Fh1<sup>fl/fl</sup> kidney epithelial cells treated with vehicle control (DMSO) and 500 micromolar thenoyltrifluoroacetone (TTFA). Five biological replicates per condition. </p> <p>5. Western blot uncropped blots</p>
Data from: Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure–activity relationship
Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure–activity relationships (QSARs) for CAAS compounds against Aspergillus niger (A. niger) and Penicillium citrinum (P. citrinum) were analysed. The QSAR models (R2 = 0.9346 for A. niger, R2 = 0.9590 for P. citrinum,) were constructed and validated. The models indicated that the molecular polarity and the Max atomic orbital electronic population had a significant effect on antifungal activity. Based on the best QSAR models, two new compounds were designed and synthesized. Antifungal activity tests proved that both of them have great bioactivity against the selected fungi.
Raw NMR for Selective and Quantitative Functionalization of Unprotected -Amino Acids Using a Recyclable Homogeneous Catalyst
<p>Raw NMR data for the article "Selective and Quantitative Functionalization of Unprotected -Amino Acids Using a Recyclable Homogeneous Catalyst"</p>
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