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1,204 results for “enzymes”
Soil extracellular enzyme activity increases during the transition from conventional to organic farming
<p>Dataset of manuscript entitled “Soil extracellular enzyme activity increases during the transition from conventional to organic farming”. This manuscript includes the results of WP1 from the SOFT project (ref. 890874).</p>
Extracellular polymeric substances are closely related to land cover, microbial communities, and enzyme activity in tropical soils
<p>These are datasets and R codes linked to the paper: Extracellular polymeric substances are closely related to land cover, microbial communities, and enzyme activity in tropical soils. </p>
Catalytic Rules and Validation Results for "EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions"
<p>Dataset containing the "Rules of Enzyme Catalysis" as created during the development of EzMechanism and the validation results of the software. For more information see https://www.biorxiv.org/content/10.1101/2022.09.05.506575v1, and the M-CSA website in https://www.ebi.ac.uk/thornton-srv/m-csa/</p>
Soil extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the N fertilized and reference watershed at the Fernow Experimental Forest, WV.
Our objective was to detect possible differences in N fertilization responses of soil extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated 10 x 10 m plots in both the reference and N fertilized watersheds (N=24 plots) at the Fernow Experimental Forest, Parsons, WV. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). In addition, we measured microbial allocation to complex C degrading oxidative enzymes phenol oxidase and peroxidase. The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils during the growing season in 2017.
Extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the nitrogen fertilized and reference watershed at the Bear Brook Watershed in Maine, USA during the final year of N fertilization (2016) and during the year after N fertilization ceased (2017).
Our objective was to detect possible differences in N fertilization responses of extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated (>65% diameter at breast height) 10 x 10 m plots in the lower elevation hardwood zone of both the reference and N fertilized watersheds (N=24 plots) at Bear Brook Watershed, in Maine USA. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils in the final year of N fertilization at Bear Brook in 2016 and during the year after N fertilization ceased in 2017.
Extracellular enzyme activities in soils from Arctic LTER moist acidic tundra nutrient addition plots, Toolik Field Station, Alaska, sampled July 2011.
Soil samples were collected from control, and N+P plots from within a set of treatments in Arctic LTER Moist Acidic Tundra plots established in 1989 and in 2006 . At the time of sampling the soil was separated into organic horizon, organic/mineral interface, and the upper 5cm of the mineral soil. In the lab the potential activities of seven hydrolytic enzymes was determined using fluorometric techniques (Saiya-Cork et al. 2002) modified following Steinweg et al(.2012).
Comparison of polyphenol degrading enzyme activities between forest types and soil horizons from 2003 to 2004
In the southern Appalachians Rhododendron maximum thickets suppress conifer and hardwood regeneration. While there has been research on the effects of R. maximum on physical and chemical environment, the functioning of R. maximum ericoid mycorrhizas has been unexplored. The litter of ericaceous plants tends to be rich in phenolic compounds. These compounds can form recalcitrant complexes with various forms of organic N, and may be responsible for lowering decomposition and N mineralization rates. While polyphenol-organic N complexes are highly recalcitrant, some fungi, particularly ericoid mycorrhizal fungi, have the ability to access this sequestered N. Since the litter of ericaceous plants is rich in phenolic compounds and ericoid mycorrhizal fungi are equipped to degrade phenolic compounds, polyphenol-organic N complexing may represent an N cycling strategy that prevents non-ericaceous plants from accessing sources of organic N. We propose to examine the activities of polyphenol degrading enzymes in the soil of R. maximum thickets and neighboring hardwood forests.
Climate Change Across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest: growth and enzyme activity traits of soil fungi isolated from CCASE in July 2017, grown under a common garden experiment in the laboratory that mimicked CCASE soil temperature treatments
Projections for the northeastern U.S. indicate that mean air temperatures will rise and snowfall will become less frequent, causing more frequent soil freezing. To test fungal responses to these combined chronic and extreme soil temperature changes, we conducted a laboratory-based common garden experiment with soil fungi that had been subjected to different combinations of growing season soil warming, winter soil freeze/thaw cycles, and ambient conditions for four years in the field. We found that fungi originating from field plots experiencing a combination of growing season warming and winter freeze/thaw cycles had inherently lower activity of acid phosphatase, but higher cellulase activity, that could not be reversed in the lab. In addition, fungi quickly adjusted their physiology to freeze/thaw cycles in the laboratory, reducing growth rate and potentially reducing their carbon use efficiency. Our findings suggest that less than four years of new soil temperature conditions in the field can lead to physiological shifts by some soil fungi, as well as irreversible loss or acquisition of extracellular enzyme activity traits by other fungi. These findings could explain field observations of shifting soil carbon and nutrient cycling under simulated climate change. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Fig. 2 in Changes in digestive enzymes activities during the initial ontogeny of wolf cichlid, Parachromis dovii (Perciformes: Cichlidae)
Fig. 2. Digestive proteolytic enzyme activity during ontogeny of Parachromis dovii larvae (means ± SD, n= 3 replicates). (a) specific acid proteolytic activity, (b) specific alkaline proteolytic activity, (c) specific trypsin activity, (d) specific chymo- trypsin activity, (e) specific leucine-aminopeptidase activity, (f) specific carboxypeptidase A activity.
All atom simulations snapshots and contact maps analysis scripts for SARS-CoV-2002 and SARS-CoV-2 spike proteins with and without ACE2 enzyme
<p><strong>The dataset contains a total of 40 snapshots of the four trajectories (10 snapshots each system = two per replica x 5 replicas/system):</strong></p> <ol> <li>SARS-CoV-2002 spike protein without ACE2</li> <li>SARS-CoV-2 spike protein without ACE2</li> <li>SARS-CoV-2002 spike protein with ACE2</li> <li>SARS-CoV-2 spike protein with ACE2</li> </ol> <p>Molecular dynamics simulation trajectories (320ns each) have been performed using the Amber ff14SB force field running with the Amber18 package at the the NSF-funded (OAC-1826915, OAC-1828163) ELSA high performance computing cluster at The College of New Jersey. Under the following simulation methodology:</p> <p><em>All-atom simulations were carried out with Amber18 (<a href="https://slack-redir.net/link?url=http%3A%2F%2Fambermd.org">ambermd.org</a>), and system components (protein, ions, water) were modeled with the included FF14SB and TIP3P parameter sets. Energy minimization used CPU pmemd, while later simulation stages used GPU pmemd. CoV2 and CoV1 systems with one RBD up (with/without ACE2) were solvated in 12 angstrom water shells. Cysteine residues identified in the initial models as having a disulfide bond (DB) were bonded using tLeap. All simulations used 0.150 M NaCl. Hydrogen mass repartitioning was applied only to the protein to enable a 4 fs timestep (<a href="https://slack-redir.net/link?url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Fct5010406">https://pubs.acs.org/doi/abs/10.1021/ct5010406</a>). The SHAKE algorithm was applied to hydrogens, and a real-space cutoff of 8 angstroms was used. Periodic boundary conditions were applied and PME was used for long-range electrostatics. Minimization was by steepest descent (2000 steps) followed by conjugate gradient (3000 steps). Heating used two stages: (1) NVT heating from 0 K to 100 K (50 ps), and (2) NPT heating from 100 K to 300 K (100 ps). Restraints of 10 kcal mol<sup>-1</sup> angstrom<sup>-2</sup> were applied during minimization and heating to C-alpha atoms. During 6 ns of equilibration at 300 K C-alpha restraints were gradually reduced from 10 kcal mol<sup>-1</sup> angstrom<sup>-2</sup> to 0.1 kcal mol<sup>-1</sup> angstrom<sup>-2</sup>. Finally, restraints were released and 320 ns unrestrained production simulations were carried out for CoV2 and CoV1 systems. Production simulations began from the final equilibrated snapshots, and five copies of each system were simulated. As unrestrained systems can freely rotate we monitored simulations for any close contacts and found that in one copy of the CoV1 simulation without ACE2 and one RBD up that a few contacts close to 8 angstrom occur near the end of the 320 ns between the RBD and a different subdomain of the spike complex in a periodic image. However this did not influence analyzed structural properties which is verified by comparing results across simulations. The Monte Carlo barostat was used to maintain pressure (1 atm), and the Langevin thermostat was used to maintain 300 K temperature (collision frequency 1 ps<sup>-1</sup>), as implemented in Amber18. In aggregate, nearly 7 microseconds of simulation of systems ranging from 396,147 to 879,100 atoms was carried out for this work.</em><br> For further details on the trajectories, please contact Joseph Baker (bakerj@tcnj.edu).</p> <p><strong>Regarding the contact map analysis scripts (contactMaps_Analysis.tar.gz), they contain the following workflow:</strong></p> <p>contactmap --> source files from contact_map executable<br> process_nc.sh --> convert raw data from all-atom simulation to numbered PDB files and get the contact maps<br> frequency.lua --> read a set of PDB files and output the frequency count for each contact<br> consensus.fasta --> align sequence of Covid19 and SARS from Chimera<br> consensus.lua --> read data previously generated and compute the frequency per residue, among other things.<br> consensus.sh --> input information to consensus.lua<br> consensus.gp --> gnuplot script to plot figures</p> <p>This dataset and the code is part of tripartite collaboration between:</p> <ul> <li>The Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland (supported by the National Science Centre, Poland, under grant No. 2017/26/D/NZ1/0046)</li> <li>Department of Chemistry, The College of New Jersey, New Jersey, United States (supported by National Science Foundation under grant numbers OAC-1826915 and OAC-1828163).</li> <li>Jozef Stefan Institute, Ljubljana, Slovenia (supported by the Slovenian Research Agency (Funding No. P1-0055)).</li> </ul>
Simple structural views of the SARS spike glycoprotein complex with human angiotensin-converting enzyme 2 (ACE2)
<p>A set of 5 screenshots of UnityMol running the first example system. Three screenshots are from a multi-user virtual reality session with 3 participants, two screenshots illustrate a custom menu to drive the example more efficiently and make it simple for the end user.</p>
Research data supporting "Enzyme Prodrug Therapy Engineered into Electrospun Fibers with Embedded Liposomes for Controlled, Localized Synthesis of Therapeutics"
<p>Research data supporting the publication: Chandrawati R. et al., 2017, Enzyme Prodrug Therapy Engineered into Electrospun Fibers with Embedded Liposomes for Controlled, Localized Synthesis of Therapeutics, Advanced Healthcare Materials. DOI: 10.1002/adhm.201700385</p>
Figure 1 in Effects of commercial oils on the camel tick, Hyalomma dromedarii (Acari: Ixodidae) and their enzyme activities
Figure 1. Mortality percentages of Hyalomma dromedarii semi-engorged females treated with different concentrations of four oils at five successive days after treatment – A. Rosemary; B. Garlic; C. Neem; D. Cyperus. a, b, … etc. indicate significant differences between concentrations (%) of each oil for each day according to Tukey test (P <0.001).
Dataset from the analysis of biological activity of endophytic strain Serratia quinivorans KP32, the expression of biocontrol-related genes and the activity of antioxidant enzymes in bacterial cells treated with pathogenic fungi filtrates
<p>This dataset contains the data from the analyses published in the article entitled "Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain <i>Serratia quinivorans</i> KP32 to Fungal Phytopathogens" in the International Journal of Molecular Sciences (https://doi.org/10.3390/ijms232415561). The data consist of results collected for studies on the antifungal activity of KP32 strain towards four fungal phytopathogens, results of primer efficiency determination and studies on the expression of genes potentially involved in biocontrol after treatment of KP32 strain with the fungal phytopathogens filtrates. Additionally, absorbances from activity tests for catalase (CAT) and superoxide dismutase (SOD) in the strain treated with fungal pathogens are included.</p>
Dataset for "Exploring the Potential of Various Cyclodextrin-based Derivatives in Enzyme Supramolecular Engineering" research article
<p>The dataset for the paper titled "Exploring the Potential of Various Cyclodextrin-based Derivatives in Enzyme Supramolecular Engineering".<br>The dataset includes the following items:<br><br>1. "alpha-CD-TES_Characterization" xls file (1 file) including 5 datasheets;<br>These data sheets provide raw characterization data regarding the synthesis of the alpha-CD-TES molecule including 1H NMR, 13C NMR, FTIR, ESI-MS, and MALDI.</p> <p>2. "beta-CD-TES_Characterization" xls file (1 file) including 5 datasheets;<br>These data sheets provide raw characterization data regarding the synthesis of the beta-CD-TES molecule including 1H NMR, 13C NMR, FTIR, ESI-MS, and MALDI.</p> <p>3. "gamma-CD-TES_Characterization" xls file (1 file) including 5 datasheets;<br>These data sheets provide raw characterization data regarding the synthesis of the gamma-CD-TES molecule including 1H NMR, 13C NMR, FTIR, ESI-MS, and MALDI.<br><br>4. "Activities" xls file (1 file) including 6 datasheets;<br>These datasheets contain the raw data of the enzymatic activities measured for both LipMRD9 and A50 enzymes for each set of stability experiments reported in the manuscript or the supporting information documents.</p> <p>5. "Layer growth - A50" zip file including 5 files:<br>The unprocessed SEM micrographs of A50 enzyme shielding with alpha/beta/gamma-CD-TES building blocks (after 75 min reaction) and the corresponding size measurements in an xls file.</p> <p>6. "Layer growth - LipMRD9" zip file including 15 files:<br>The unprocessed SEM micrographs of the shielded LipMRD9 enzyme with α-, β-, and γ-CD-TES building blocks (after 30, 60, 90, and 120 min reaction) and the corresponding size measurements (using ImageJ software) saved in separate xls files.</p>
Supplementary Dataset for Deep learning based kcat prediction enables improved enzyme constrained model reconstruction
<p>This dataset is the supplementary dataset for the paper "<strong>Deep learning based <em>k</em><sub>cat</sub> prediction enables improved enzyme constrained model reconstruction</strong>". Protein sequence fasta files, deep learning predicted <em>k</em><sub>cat</sub> values, classcial-ecGEMs, DL-ecGEMs and <em>Posterior</em>-mean-ecGEMs for 343 yeast/fungi species are available in this dataset.This repository also contains the computed results for reproducing the figures as model_build_files . The scripts can be found in Github (https://github.com/SysBioChalmers/DLKcat)</p>
Sequence Similarity Network (SSN) and Genome Neighbourhood Network (GNN) for Mycobacterium Cytochrome P450 enzymes
<p>This dataset was generated in the context of the Horizon 2020 MSCA IF action deCrYPtion (Grant 839116). The aim of this project is to use comparative genomics in order to propose and then test the function of uncharacterised Cytochrome P450 enzymes that are present among Mycobacterium species.</p> <p>More information about this project can be found at: https://cordis.europa.eu/project/id/839116.</p> <p>This dataset contains:</p> <p>- The FASTA sequences files obtained from the UniProt database, for members of the PF00067 protein family (CYP).</p> <p>- A set of reference FASTA sequences, matching the supplementary material from the following publication: Parvez, M. <em>et al.</em> (2016) ‘Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s’, <em>Scientific Reports</em>, 6(1), p. 33099. doi:<a href="https://doi.org/10.1038/srep33099">10.1038/srep33099</a>.</p> <p>- A combined FASTA files of both previously described, that was used for the generation of SSNs</p> <p>- A PNG image produced from the analysis of the Sequence Similarity Networks generated at AST78 (corresponding to 40% identity, defining CYP families)</p> <p>- A PNG image produced from the analysis of the Sequence Similarity Networks generated at AST141 (corresponding to 55% identity, defining CYP subfamilies)</p> <p>- A Cytoscape session for the Sequence Similarity Networks from the combined FASTA file generated using the Enzyme Function Initiative web tools (https://efi.igb.illinois.edu), at AST78</p> <p>- A Cytoscape session containing Sequence Similarity Networks and Genome Neighborhood Network from the combined FASTA file generated using the Enzyme Function Initiative web tools (https://efi.igb.illinois.edu), at AST141</p>
Code and Data associated with "Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment with Escherichia coli"
<p>Code and data sufficient to reproduce analyses in "Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment with <em>Escherichia coli</em>".</p>
Precision synthesis of reducing-end thiol-modified cellulose enabled by enzyme selection
<p>We provide here the underlying data of the publication "Precision synthesis of reducing-end thiol-modified cellulose enabled by enzyme selection". Please find the abstract below.</p> <p>Enzyme-catalyzed iterative <em>β</em>-1,4-glycosylation of <em>β</em>-glycosides is promising for bottom-up polymerization of reducing-end-modified cello-oligosaccharide chains. Self-assembly of the chains from solution yields crystalline nanocellulose materials with properties that are tunable by the glycoside group used. Cellulose chains with a reducing-end thiol group are of interest to install a controllable pattern of site-selective modifications into the nanocellulose material. Selection of the polymerizing enzyme (cellodextrin phosphorylase; CdP) was pursued here to enhance the synthetic precision of <em>β</em>-1-thio-glucose conversion to generate pure “1-thio-cellulose” (≥95%) unencumbered by plain (unlabeled) cellulose resulting from enzymatic side reactions. The CdP from <em>Clostridium stercorarium</em> (<em>Cs</em>CdP) was 21 times more active on <em>β</em>-1-thio-glucose (0.17 U/mg; 45 °C) than the CdP from <em>Clostridium cellulosi</em> (<em>Cc</em>CdP), and it lacked hydrolase activity, which is substantial in <em>Cc</em>CdP, against the α-D-glucose 1-phosphate donor substrate. The combination of these enzyme properties indicated that <em>Cs</em>CdP is a practical catalyst for 1-thio-cellulose synthesis directly from <em>β</em>-1-thio-glucose (8 h; 25 mol% yield) that does not require a second enzyme (cellobiose phosphorylase), which was essential when using the less selective <em>Cc</em>CdP. The 1-thio-cellulose chains had an average degree of polymerization of ∼10 and were assembled into highly crystalline cellulose II crystallinity material.</p>
Enzyme Substrate Classification Dataset for SDRs and SAM-MTases
<p>This dataset contains sequence information, three-dimensional structures (from AlphaFold2 model), and substrate classification labels for 358 short-chain dehydrogenase/reductases (SDRs) and 953 S-adenosylmethionine dependent methyltransferases (SAM-MTases).</p> <p>The aminoacid sequences of these enzymes were obtained from the UniProt Knowledgebase (https://www.uniprot.org). The sets of proteins were obtained by querying using InterPro protein family/domain identifiers corresponding to each family: IPR002347 (SDRs) and IPR029063 (SAM-MTases). The query results were filtered by UniProt annotation score, keeping only those with score above 4-out-of-5, and deduplicated by exact sequence matches.</p> <p>The structures were submitted to the publicly available AlphaFold2 protein structure predictor (J. Jumper et al., Nature, 2021, 596, 583) using the ColabFold notebook (https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.1-premultimer/batch/AlphaFold2_batch.ipynb, M. Mirdita, S. Ovchinnikov, M. Steinegger, Nature Meth., 2022, 19, 679, https://github.com/sokrypton/ColabFold). The model settings used were msa_model = MMSeq2(Uniref+Environmental), num_models = 1, use_amber = False, use_templates = True, do_not_overwrite_results = True. The resulting PDB structures are included as ZIP archives</p> <p>The classification labels were obtained from the substrate and product annotations of the enzyme UniProtKB records. Two approaches were used: substrate clustering based on molecular fingerprints and manual substrate type classification. For the substate clustering, Morgan fingerprints were generated for all enzymatic substrates and products with known structures (excluding cofactors) with radius = 3 using RDKit (https://rdkit.org). The fingerprints were projected onto two-dimensional space using the UMAP algorithm (L. McInnes, J. Healy, 2018, arXiv 1802.03426) and Jaccard metric and clustered using k-means. This procedure generated 9 clusters for SDR substrates and 13 clusters for SAM-MTases. The SMILES representations of the substrates are listed in the SDR_substrates_to_cluster_map_2DIMUMAP.csv and SAM_substrates_to_13clusters_map_2DIMUMAP.csv files.</p> <p><br> The following manually defined classification tasks are included for SDRs: NADP/NAD cofactor classification; phenol substrate, sterol substrate, coenzyme A (CoA) substrate. For SAM-MTases, the manually defined classification tasks are: biopolymer (protein/RNA/DNA) vs. small molecule substrate, phenol subsrates, sterol substrates, nitrogen heterocycle substrates. The SMARTS strings used to define the substrate classes are listed in substructure_search_SMARTS.docx.<br> </p>
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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.