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934 results for “Amino acids”
Nitrogen isotope ratios of nitrate, ammonium, and amino acids in sinking particles in the Northwestern North Pacific
<p>The database includes sample information and nitrogen isotope measurements of nitrate, ammonium, and amino acids in sinking particles in the Northwestern North Pacific. The sinking particles were collected in sediment traps moored at depths of 200, 500, and 4,810 m at station K2 (47°N, 160°E; water depth, ~5,200 m). The seawater was sampled with a plastic bucket for the surface and Niskin-X sampling bottles for water below the surface at stations K2 and KNOT (44°N, 155°E). The model package of a 1D nitrogen isotope model includes model source code written in Fortran 90, forcing, and initial condition at station K2.</p>
Essential amino acid requirements of granivorous and omnivorous songbirds and the provision of natural foods
<p>Wild birds must consume certain amounts of protein and an appropriate balance of amino acids while inhabiting environments where foods often differ in the quantity and quality of available protein. The requirements for amino acids are well documented for domestic bird species but are largely unknown for wild birds, which makes it impossible to reliably assess the nutritional adequacy of foods eaten by wild birds. We measured the maintenance requirements for three essential amino acids (lysine, methionine, and arginine) in two species of songbird, the omnivorous Hermit Thrush (<i>Catharus guttatus</i>) and granivorous White-throated Sparrow (<i>Zonotrichia albicollis</i>). Hermit Thrushes and White-throated Sparrows had similar requirements for lysine (20.02 and 19.95 mg/day, respectively) and methionine (12.3 and 10.85 mg/day, respectively), whereas thrushes had lower requirements for arginine (18.07 mg/day) compared to sparrows (34.5 mg/day). Consistent with previous studies, most birds fed diets with inadequate essential amino acid concentrations reduced food intake and fecal output, lost body mass, and had lower, but not negative nitrogen balance. However, we provide the first evidence that songbirds overcompensate when they consume diets very deficient in lysine. Available data on amino acid concentrations in natural foods suggests that most insects contain relatively high concentrations of all essential amino acids, seeds likely satisfy requirements of lysine and arginine but not methionine for Hermit Thrushes and White-throated Sparrows, whereas fruits generally contain inadequate amounts of all essential amino acids. Therefore, birds that eat mostly fruit may consume enough protein but likely must eat other types of foods to satisfy their essential amino acid requirements.</p>
Raw data for the article "Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization"
<p>Raw NMR, HPLC and MS data for the article "Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization" published in Angewandte Chemie, DOI: </p> <p><a href="https://doi.org/10.1002/anie.202404747">https://doi.org/10.1002/anie.202404747</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>
Iterative Arylation of Amino Acids and Aliphatic Amines via δ‐C(sp3)−H Activation: Experimental and Computational Exploration
<p>This dataset contains the geometries of all optimized structures (in <em>.xyz</em> format with their associated energy in Hartrees) accompanying the paper "Iterative Arylation of Amino Acids and Aliphatic Amines via δ‐C(sp3)−H Activation: Experimental and Computational Exploration" published in Angew. Chem. Int. Ed.. doi:<a href="https://doi.org/10.1002/anie.201900479">10.1002/anie.201900479</a> on 28 Feb 2019.</p>
Understanding Titan's Prebiotic Chemistry: Synthesizing Amino Acids through Aminonitrile Alkaline Hydrolysis
<p>This folder accompanies the study titled, “Understanding Titan’s Prebiotic Chemistry: Synthesizing Amino Acids through Aminonitrile Alkaline Hydrolysis” by Farnsworth et al. Here, you will find an excel file with two tabs that provides the raw data used to create the two LCMS figures in the paper. Thanks, and enjoy!</p>
Predicting the solubility of amino acids and peptides with the SAFT-γ Mie approach: Neutral and charged models
<p>Calculated data accompanying the IECR 2024 publication "Predicting the Solubility of Amino Acids and Peptides with the SAFT‑γ Mie Approach: Neutral and Charged Models", by Ahmed Alyazidi, Shubhani Paliwal, Felipe A. Perdomo, Amy Mead, Mingxia Guo, Jerry Y. Y. Heng, Thomas Bernet, Andrew Haslam, Claire S. Adjiman, George Jackson, and Amparo Galindo. </p>
Bulk and amino acid nitrogen specific isotope data from particulate organic matter and mesozooplankton (1000-2000 µm) from the Mekong River plume and southern South China Sea
<p><strong><span><span>The mean trophic position (TP) of mesozooplankton largely determines how much mass and energy is available for higher trophic levels like fish. Unfortunately, the ratio of herbivores to carnivores in mesozooplankton is difficult to identify in field samples. Here we investigated changes in the mean TP of mesozooplankton in a highly dynamic environment encompassing four distinct habitats in </span></span></strong>the southern South China Sea:<strong> </strong><span>the </span>Mekong River plume, coastal upwelling region, shelf waters, and offshore oceanic waters<strong><span>. </span></strong><span>We used a set of parameters derived from bulk and amino acid nitrogen stable isotopes from particulate organic matter (POM) and four mesozooplankton size fractions to identify changes in the nitrogen source and structure of the planktonic food web across these habitats.</span> We found clear indications of a shift in N sources for biological production from nitrate in near-coastal waters towards an increase in diazotroph-N inputs in oceanic waters where diazotrophs shaped the phytoplankton community. The shift in N source was accompanied by a lengthening of the food chain (increase in the TP), which may provide further support for the connection between diazotrophy and the indirect routing of N through the marine food web. Our combined bulk and amino acid δ<sup>15</sup>N approach also allowed us to estimate the trophic enrichment (TE) of mesozooplankton across the entire regional ecosystem. When put in the context of literature values, our high TE of 5.1‰ suggested a link between ecosystem heterogeneity and the less efficient transfer of mass and energy across trophic levels.</p>
The importance of kelp to an intertidal ecosystem varies by trophic level: insights from amino acid δ13C analysis
<p>A fundamental question in ecology is understanding how energy and nutrients move through and between food webs, and which sources of production support consumers. In marine ecosystems, these basic questions have been challenging to answer given the limitation of observational methods. Stable isotope analysis of essential amino acids (EAA δ<sup>13</sup>C) has great potential as a tool to quantify energy and nutrient flow through marine food webs; however, it has been primarily utilized at large spatial scales. Here, we used EAA δ<sup>13</sup>C analysis to test for connectivity between adjacent subtidal and intertidal components of a nearshore ecosystem in south central Alaska. We measured δ<sup>13</sup>C of six EAA from four marine producer groups: subtidal kelp (<i>Laminaria</i> sp.), offshore particulate organic matter (POM), and intertidal red (<i>Neorhodomela</i> sp.) and green (<i>Ulva</i> sp.) algae. In addition, we sampled four intertidal invertebrate consumer species spanning a range of trophic/functional groups: <i>Mytilus</i> sp., <i>Strongylocentrotus droebachiensis</i>,<i> Nucella</i> sp., and <i>Pycnopodia helianthoides</i>. Using canonical analysis of principal coordinates (CAP) and isotope mixing models (MixSIAR), we tested for differences among producer EAA δ<sup>13</sup>C fingerprints and quantified the contribution of producer EAA to consumers. We compared these results to previously published EAA δ<sup>13</sup>C data on marine producers to examine the generality of this technique. We found the EAA δ<sup>13</sup>C fingerprints of subtidal kelps (<i>Laminaria</i>), <i>Ulva,</i> and <i>Neorhodomela</i> were highly distinct from one another. Further, our measured EAA δ<sup>13</sup>C patterns for kelp and red algae matched those previously reported from other localities, suggesting unique and universal EAA δ<sup>13</sup>C signatures for these groups. However, CAP could not distinguish between microalgae (POM) and <i>Ulva</i>, possibly due to similar biochemical pathways for the synthesis of EAA. Using these producer fingerprints, we found upper trophic-level invertebrate consumers, <i>Nucella</i> and <i>Pycnopodia</i>, derived more than 60% of their essential amino acids from subtidal kelps. In contrast, the sampled primary consumers in the system, <i>Mytilus</i> and <i>Strongylocentrotus</i>, relied more heavily on <i>Ulva</i> and/or offshore POM. Our results provide evidence for connectivity between two adjacent nearshore ecosystems and exemplify EAA δ<sup>13</sup>C as a powerful new tool in tracing energy and nutrient flow within and among marine food webs.</p>
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).
Chiral Phosphoric Acid Catalyzed Asymmetric Hydrolysis of Biaryl Oxazepines for the Synthesis of Axially Chiral Biaryl Amino Phenol Derivatives
<p>This folder /DFT_structures/ contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</p> <p>"Chiral Phosphoric Acid Catalyzed Asymmetric Hydrolysis of Biaryl Oxazepines for the Synthesis of Axially Chiral Biaryl Amino Phenol Derivatives"</p> <p>Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1 (sometimes omitted), c2, c3, ...</p> <p>This folder contains the following sub-folders:</p> <p>- /irc_movies/ contains movies of the IRC analyses for the rotational barrier TSs;</p> <p>- /structures/ contains the DFT-optimized structures</p>
Steady-state and time-resolved data for the article "Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222"
<p>1. Steady-state data</p> <p>Spectra were taken with/without continuous irradiation with a wavelength of 450 nm.</p> <p>1.1 CNF absorption region (2200-2260 cm<sup>-1</sup>)</p> <p>1.2. Amide absorption region (1500-1800 cm<sup>-1</sup>)</p> <p>1.3. UV/Visible absorption region (320-550 nm)</p> <p>Each spectral region has 3 datasets:</p> <p>- DARK</p> <p>- LIT (photostationary state)</p> <p>- DIFFERENCE (lit-minus-dark)</p> <p>The first row contains the variants.</p> <p>The first column contains the wavenumber (in cm<sup>-1</sup>) or wavelength (in nm).</p> <p>2. Time-resolved data.</p> <p>Dark recovery reaction after switching lights off (wavelength of 450 nm).</p> <p>2.1. EL222_WT_H2O</p> <p>2.2. EL222_WT_D2O</p> <p>2.3. EL222_W31CNF</p> <p>2.4. EL222_L35CNF</p> <p>2.5. EL222_N53CNF</p> <p>2.6. EL222_Y136CNF</p> <p>2.7. EL222_M151CNF</p> <p>2.8. EL222_L216CNF</p> <p>2.9. EL222_LOV_H2O</p> <p>2.10. EL222_LOV_D2O</p> <p>For each variant we have measured 3 spectral regions (except for 2.1, 2.2., 2.9 and 2.10, which lack CNF):</p> <p>- CNF: 2200-2270 cm<sup>-1</sup></p> <p>- AMIDE: 1500-1750 cm<sup>-1</sup></p> <p>- UVVIS: 320-550 nm</p> <p>For each probe we have 2 datasets:</p> <p>- DATA: the experimental lit-minus-dark absorbance difference spectra. </p> <p>The first row contains the time delays (in seconds).</p> <p>The first column contains the wavenumbers (in cm<sup>-1</sup>) or wavelength (in nm).</p> <p>- LDA: the lifetime density maps calculated from the corresponding DATA using the inverse Laplace transform and maximum entropy penalty.</p> <p>The first row contains the lifetimes (in seconds).</p> <p>The first column contains the wavenumbers (in cm<sup>-1</sup>) or wavelength (in nm).</p> <p>If you use these datasets please cite:</p> <p>Chaudhari, A.S.; Chatterjee, A.; Domingos, C.A.O.: Andrikopoulos, P. C.; Liu, Y.; Andersson, I.; Schneider, B.; Lórenz-Fonfría, V.A.; Fuertes, G. Genetically Encoded Non-canonical Amino Acids Reveal Asynchronous Dark Reversion of Chromophore, Backbone and Side-chains in EL222. <em>Protein Science</em>. 2023 <a href="https://doi.org/10.1002/pro.4590">https://doi.org/10.1002/pro.4590</a></p>
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species
<p>Income and capital breeding represent opposing ends of a continuum of reproductive strategies. Quantifying nutrient allocation to reproduction is challenging, but recent advances in compound-specific stable isotope analysis hold promise for tracing the source of individual compounds allocated to reproduction. </p> <p>Here, we describe a novel approach of using measured carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) isotope values of individual amino acids (AAs) in pectoral muscle of egg-laying females and egg yolk as a useful tool to quantify the reliance on income versus capital breeding in migrating species. We used white-fronted (<em>Anser albifrons frontalis</em>), lesser snow (<em>A. caerulescens caerulescens</em>), and black brant (<em>Branta bernicla nigricans</em>) geese breeding in tundra ecosystems of northern Alaska as model organisms.</p> <p>All three species relied on mixed capital-income breeding strategies, but models based on AA isotope data estimated higher proportional contributions of endogenous resources to yolk synthesis compared to results based on bulk tissue isotope analyses. </p> <p>Tracing income versus capital nutrient allocation in migratory species at the compound level is a major advance from the current 'elemental' perspective obtained from bulk tissue stable isotope analyses. Our framework is applicable to all taxonomic groups, as long as there is a sufficient spatial or temporal isotopic gradient between resources obtained during the breeding and non-breeding periods.</p>
Dataset from Nature Catalysis paper: Electrosynthesis of amino acids from NO and α-keto acids using two decoupled flow reactors
<p>Dataset from Nature Catalysis paper: Electrosynthesis of amino acids from NO and α-keto acids using two decoupled flow reactors</p>
Fig. 4. Amino acid sequences alignment between TCS1 and candidate N in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain
Fig. 4. Amino acid sequences alignment between TCS1 and candidate N-methyltransferase genes (GCS1, GCS2, and GCS3).
Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a in Phylogeny and domain architecture of plant ribosome inactivating proteins
Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. Colours indicate amino acids conserved in at least 70% of sequences. For the two pink-highlighted proteins, the black bolded amino acids were present in 70% of sequences at that position but were not present in the amino acid sequence of the crystal structure. (A) Sequence alignment. RIP domain consensus: the consensus sequence generated from the multiple sequence alignment in Jalview excluding gaps; 1QCI: the amino acid sequence of pokeweed antiviral protein (protein databank: 1QCI). The third line denotes the similarity in the two sequences as determined by Clustal Omega. (B) The crystal structure of 1QCI visualized in UCSF ChimeraX in surface representation; (C) mesh representation; and (D) cartoon representation. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Mycosporine-like amino acids, brominated and sulphated phenols: Suitable chemotaxonomic markers for the reassessment of classification of Bostrychia calliptera (Ceramiales, Rhodophyta)
Fig. 3. Side view (parallel to the b axis; top) and plan view (bottom) of the 2D coordination polymer of compound 5. Na atoms are drawn as balls and H atoms are omitted for clarity.
Fig. 6 in Mycosporine-like amino acids, brominated and sulphated phenols: Suitable chemotaxonomic markers for the reassessment of classification of Bostrychia calliptera (Ceramiales, Rhodophyta)
Fig. 6. HPLC chromatograms of selected Bostrychia calliptera MeOH/H2O extracts at 280 nm. Assignment of the compounds is according to Figure 1 (compound 3 to 6) and compound iii (λmax 228 nm) is unidentified, column: YMC- Pack Pro C18 RS (150 × 4.60 mm, 3 μm); mobile phase:20 mM ammonium formate and 0.6% (v/v) formic acid in water (A) and methanol (B); gradient: 0–15 min: 2% B, 23 min: 10% B, 30 min: 15% B, 35–40 min: 98% B, 40.1–50 min: 2% B; flow rate = 0.6 mL/min; T = 20 °C.
Fig. 2 in Mycosporine-like amino acids, brominated and sulphated phenols: Suitable chemotaxonomic markers for the reassessment of classification of Bostrychia calliptera (Ceramiales, Rhodophyta)
Fig. 2. Asymmetric unit of compound 5 with non-H atoms represented as thermal ellipsoids drawn at the 50% probability level. H atoms are drawn as spheres of random size.
Fig. 5 in Mycosporine-like amino acids, brominated and sulphated phenols: Suitable chemotaxonomic markers for the reassessment of classification of Bostrychia calliptera (Ceramiales, Rhodophyta)
Fig. 5. HPLC chromatograms of selected Bostrychia calliptera MeOH/H2O extracts at 310 nm. Assignment of the compounds: (i) unidentified MAA with λmax 332 nm, (ii) unidentified MAA with λmax 308 nm, (1) compound 1 (porphyra- 334), (2) compound 2 (palythine-threonine), column: YMC-Pack Pro C18 RS (150 × 4.60 mm, 3 μm) mobile phase:20 mM ammonium formate and 0.6% (v/ v) formic acid in water (A) and methanol (B); gradient: 0–15 min: 2% B, 23 min: 10% B, 30 min: 15% B, 35–40 min: 98% B, 40.1–50 min: 2% B; flow rate = 0.6 mL/min; T = 20 °C.
ScienceDex guides
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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.