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1,204 results for “Enzyme”
Leak-resilient enzyme-free nucleic acid dynamical systems through shadow cancellation
<p>DNA strand displacement (DSD) emerged as a prominent reaction motif for engineering nucleic acid-based computational devices with programmable behaviors. However, strand displacement circuits are susceptible to background noise that disrupts the circuit behavior, commonly known as leaks. The side effects of leaks are particularly severe in circuits with complex dynamical elements (e.g., feedback loops), as their leaks amplify nonlinearly, disrupting the circuit function. Shadow cancellation is a dynamic leak-elimination strategy originally proposed to control the leak growth in such circuits. However, the kinetic restrictions of the proposed method introduce a significant design overhead, making it less accessible. In this work, we use domain-level DSD simulations to examine the method's capabilities, the inner workings of its components, and, most importantly, robustness to practical deviations in its design requirements. First, we show that the method could stabilize the dynamics of several leak-affected catalytic and autocatalytic dynamical systems of practical importance. Then, through several probing experiments, we show that its design restrictions could be significantly relaxed without impacting the circuit function through simple adjustments to the circuit parameters. Finally, we discuss several ideas to tackle the practical challenges in applying the method to arbitrary DSD circuits, paving the way for future experimental work.</p>
EnzChemRED, a rich enzyme chemistry relation extraction dataset
<h1>Abstract</h1> <p>Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED, for Enzyme Chemistry Relation Extraction Dataset, a new training and benchmarking dataset to support the development of Natural Language Processing (NLP) methods such as (large) language models that can assist enzyme curation. EnzChemRED consists of 1,210 expert curated PubMed abstracts in which enzymes and the chemical reactions they catalyze are annotated using UniProtKB and ChEBI identifiers. We show that fine-tuning language models with EnzChemRED significantly boosts their ability to identify proteins and chemicals in text (86.30% F1 score) and to extract the chemical conversions in which they participate (86.66% F1 score), and the enzymes that catalyze those conversions (83.79% F1 score). We apply our methods to abstracts at PubMed scale to create a draft map of enzyme functions in literature to guide curation efforts in UniProtKB and the reaction knowledgebase Rhea.</p> <p><strong>Corresponding authors:</strong> Alan Bridge (alan.bridge@sib.swiss) and Zhiyong Lu (zhiyong.lu@nih.gov)</p> <h1>Content</h1> <p>This repository contains data to support the development of natural language processing (NLP) methods to mine biochemical reactions from text for Rhea and UniProt.</p>
Bacterial Community Weighted rrn Operon Copy Numbers and Enzyme Activity in Costa Rica and Alaska Soils.
<p>Datasets of bacterial community weighted rrn operon copy number and enzyme activity in Alaska and Costa Rica soils. The Alaska soils were collected from across four elevational terraces in a tidal wetland on the western coast. The Costa Rica soils were collected from plots subjected to precipitation manipulation treatments in La Selva Biological Research Station. </p> <p>The variable descriptions for the Alaska dataset are as follows: simple_id: an identifier variable. id: an identifier variable that includes terrace identity. transect_id: a variable that identifies collection transect location. BG_umol_g_h: the activity rate of beta-glucosiadase in micromoles per gram soil per hour. NAG_umol_g_h: the activity rate of N-acetyl-glucosaminidase in micromoles per gram soil per hour. LAP_umol_g_h: activity rate of leucine-aminopeptidase in micromoles per grams soil per hour. AP_umol_g_h: the activity rate of acid phosphatase in micromoles per gram soil per hour. BG_g_C: the activity rate of beta-glucosiadase in micromoles per gram soil carbon per hour. NAG-g_N: activity rate of N-acetyl-glucosaminidase in micromoles per gram soil nitrogen per hour. LAP_g_N: activity rate of leucine-aminopeptidase in micromoles per gram soil nitrogen per hour. AP_mg_P: activity rate of acid-phosphatase in micromoles per gram soil phosphorus per hour. P_mg_kg: soil phosphorus concentration in milligrams phosphorus per kilogram soil. K_mg_kg: soil potassium concentration in milligrams potassium per kilogram soil. C_pct: soil carbon concentration in percent. N_pct: soil nitrogen concentration in percent. pH: soil pH. cn_ratio: the carbon-to-nitrogen ratio of soil. cp_ratio: the carbon-to-phosphorus ratio of soil. np_ratio: the nitrogen to phosphorus ratio of soil. weighted_copy_number: the bacterial community weighted rrn operon copy number.</p> <p>The variable descriptions for the Costa Rica dataset are as follows: ID: a variable that identifies the soil core collected. Plot: a variable that identifies the experimental plot from which soils were collected. Precip: a variable that describes the precipitation manipulation treatment applied. Core: a variable that identifies whether soil cores were enclosed in mesh or not. Moisture: the soil moisture of the collected core in grams water per grams dry soil. weighted copy_number: the bacterial community weighted rrn operon copy number. AP: activity rate of acid-phosphatase in micromoles per gram soil per hour. BG: the activity rate of beta-glucosiadase in micromoles per gram soil per hour.</p> <p>Also included are files of the code used to analyze the data in the R Statistical Computing Environment.</p>
Source Data for Supplementary Information of "Expanding the substrate scope of PylRS enzymes to include non-⍺-amino acids in vitro and in vivo"
<p>The attached excel file contains the source data for LC-MS traces shown in the Supplementary Information of the paper "Expanding the substrate scope of PylRS enzymes to include non-⍺-amino acids in vitro and in vivo." Each graph is contained in a tab and labeled with the Supplementary Figure number and panel with which it is associated.</p>
Data for 'Accounting for digestion enzyme bias in Casanovo' (Melendez et al., 2024)
<p>This upload contains two archives and an explanatory README.md that accompany <a href="https://doi.org/10.1101/2024.05.16.594602">Accounting for digestion enzyme bias in Casanovo (Melendez et al., 2024)</a>. The archive named 'mgf_data' contains all of the mgf files used in the paper. The archive named 'mztab_data' contains mztab formatted sequencing (and enzyme classification) predictions from all models trained in the paper. The README file describes the structure of each archive, the contents of each mgf and mztab file, and the sections of the paper that each mgf or mztab file relates to.</p>
Figure 2 in Exogenously applied nutrients can improve the chickpea productivity under water stress conditions by modulating the antioxidant enzyme system
Figure 2. Effect of foliar application of nutrients on relative growth rate (g g-1 day-1) of chickpea genotypes in Bahawalpur (a) and Cholistan (b). Whereas D1= well watered; D2= Drought at flowering+ pod formation + grain filling stage; D3= Drought at flowering stage; DAS= days after sowing.
Figure 1 in Exogenously applied nutrients can improve the chickpea productivity under water stress conditions by modulating the antioxidant enzyme system
Figure 1. Effect of foliar application of nutrients on crop growth rate (g m-2 day-1) of chickpea genotypes in Bahawalpur (a) and Cholistan (b). Whereas D1= well watered; D2=Drought at flowering+ pod formation + grain filling stage; D3= Drought at flowering stage; DAS= days after sowing.
Fig. 3 in Effects of a pathogenic Beauveria bassiana (Hypocreales: Cordycipitaceae) strain on detoxifying and protective enzyme activities in Xylotrechus rusticus (Coleoptera: Cerambycidae) larvae
Fig. 3. Effects of infection by Beauveria bassiana strain BbCC01 on protective enzyme activity in Xylotrechus rusticus larvae over time. A. Catalase (CAT). B. Peroxidase (POD). C. Superoxide dismutase (SOD). Data are expressed as mean ± SE (n = 3). Different letters indicate significant differences between means (P <0.05).
Fig. 4 in Effects of a pathogenic Beauveria bassiana (Hypocreales: Cordycipitaceae) strain on detoxifying and protective enzyme activities in Xylotrechus rusticus (Coleoptera: Cerambycidae) larvae
Fig. 4. Change of the protein content in Xylotrechus rusticus larvae infected with Beauveria bassiana strain BbCC01. Data are expressed as mean ± SE (n = 3). Different letters indicate significant differences between means (P <0.05).
Fig. 2 in Effects of a pathogenic Beauveria bassiana (Hypocreales: Cordycipitaceae) strain on detoxifying and protective enzyme activities in Xylotrechus rusticus (Coleoptera: Cerambycidae) larvae
Fig. 2. Effects of infection by Beauveria bassiana strain BbCC01 on detoxifying enzyme activity in Xylotrechus rusticus larvae over time. A. Carboxylesterase (CarE). B. Glutathione S-transferase (GST). C. Acetylesterase (AchE). Data are expressed as mean ± SE (n = 3). Different letters indicate significant differences between means (P <0.05).
Fig. 1 in The effect of host plant species on the detoxifying enzymes of the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae)
Fig. 1. Enzymatic activity of (A) general esterase (EST), (B) glutathione S-transferase (GST), and (C) cytochrome monooxygenase P450 from Diaphorina citri reared on Citrus sinensis, Murraya paniculata, and Bergera koenigii. Means with the same letter are not significantly different from each other (P <0.05, Fisher's protected LSD test).
Fig. 3 in Effects of cold-acclimation, pathogen infection, and varying temperatures on insecticide susceptibility, feeding, and detoxifying enzyme levels in Diaphorina citri (Hemiptera: Liviidae)
Fig. 3. Correlations between mean percentage mortality of Diaphorina citri and temperature for field-collected and uninfected D. citri and field-collected and 'Candidatus' Liberibacter asiaticus–infected D. citri, when exposed to chlorpyriphos (A), fenpropathrin (B), imidacloprid (C), thiamethoxam (D), and spinetoram (E).
Fig. 1 in Effects of cold-acclimation, pathogen infection, and varying temperatures on insecticide susceptibility, feeding, and detoxifying enzyme levels in Diaphorina citri (Hemiptera: Liviidae)
Fig. 1. Comparison of cytochrome P450 (A), general esterase (B), and glutathione S-transferase (C) activity levels in laboratory susceptible Diaphorina citri adults at 5 temperatures. For glutathione S-transferase, means with the same uppercase letters are not significantly different from one another for imidacloprid-treated D. citri. Means with the same lowercase letters are not significantly different from one another for spinetoram-treated D. citri.
Research data supporting "A robust liposomal platform for direct colorimetric detection of sphingomyelinase enzyme and inhibitors"
<p>Raw research data supporting the publication: Holme, M. N. et al., ACS Nano, 2018, DOI: 10.1021/acsnano.8b03308.</p>
Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex
<p>Deregulation of the ubiquitin ligase E6AP is causally linked to the development of human disease, including cervical cancer. In complex with the E6 oncoprotein of human papillomaviruses, E6AP targets the tumor suppressor p53 for degradation, thereby contributing to carcinogenesis. Moreover, E6 acts as a potent activator of E6AP by a yet unknown mechanism. However, structural information explaining how the E6AP-E6-p53 enzyme-substrate complex is assembled, and how E6 stimulates E6AP, is largely missing. We therefore developed and applied different approaches in structural mass spectrometry to show that binding of E6 induces conformational rearrangements in E6AP, which result in the positioning of E6 and p53 in the immediate vicinity of the catalytic centre of E6AP. Our data provides structural and functional insights into the dynamics of the full-length E6AP-E6-p53 enzyme-substrate complex and reveals how E6 can both stimulate the ubiquitin ligase activity of E6AP and facilitate the transfer of ubiquitin from E6AP onto p53.</p>
Enzymes from the BRENDA database annotated with organism growth temperatures and predicted Topt
<p>Experimental as well as predicted organism growth temperatures were used to annotate enzymes from the BRENDA database (doi: 10.1093/nar/gky1048, https://www.brenda-enzymes.org) version 2018.2 (July 2018). The growth temperature annotation can be used as an estimate of the enzymes catalytic optima. In addition to this, the sequence of each enzyme was taken into account to predict catalytic optima, which are more accurate than simply using OGT as an estimate.</p> <p>The "enzyme_ogt_topt.tsv" file is a tab-separated file with the data headers: ec, uniprot_id, domain, organism, ogt, ogt_source, topt and topt_source. The ec column lists enzyme classes. The uniprot_id lists UniProt identifiers. The domain column lists the domain of life (superkingdom), either Archaea, Bacteria, or Eukarya. The organism column lists organism names, with strain designations removed and formatted to lowercase characters with an underscore _ separating the name parts. The ogt column lists, in degrees centigrade, the organism growth temperature. The ogt_source column lists whether experimental growth temperatures or predicted ones were used for the annotation. The topt column lists the enzyme catalytic optimum. Finally, the topt_source column lists whether experimental or predicted topt was used for the annotation.</p> <p>The "brenda_sequences_20180109.fasta" file follows the standard FASTA format and contains the protein sequences for all annotated enzymes. UniProt identifiers are used as a header for each of the sequences.</p> <p> </p>
Why is the Km of an enzyme half of Vmax?
<p>test</p>
Common photosinthetic enzymes from 174 metagenomes from the Malaspina Expedition 2010 (Ortega et al. 2019)
<p>Predicted genes corresponding to the four most common enzymes present in photosynthetic organisms: NADH:ubiquinone reductase (H+-translocating), N-acetyl-gamma-glutamyl-phosphate reductase, DNA-directed RNA polymerase and non-specific serine/threonine protein kinase of 174 metagenomes sequenced during the Malaspina 2010 global expedition.</p> <p>From: Alejandra Ortega, Nathan R Geraldi, Intikhab Alam, Allan A Kamau, Silvia G Acinas, Ramiro Logares, Josep M Gasol, Ramon Massana, Dorte Krause-Jensen and Carlos M Duarte. Important contribution of macroalgae to oceanic carbon sequestration. Nature Geoscience.</p>
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group. in Distribution of extracellular enzyme-producing bacteria in the digestive tracts of 4 brackish water fish species
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group.
FIGURE 4 in A typical enzyme activity for glutathione conjugation indicates exposure of pacu to pollutants
FIGURE 4 |GST specific activities in kidney cytosol from Piaractus mesopotamicus injected with benzo[a]pyrene (15 mg kg-1). Assays were carried out with 1-chloro-2,4-dinitrobenzene (CDNB), ethacrynic acid (ETHA) or 2-dichloro-4-nitrobenzene (DCNB) 7 and 14 days after the injection. Bars represent the means ± S.E.M. of determinations from nine fish injected with corn oil (clear) or benzo[a]pyrene (dark grey). Significant different from controls are indicated as *(P <0.05) and ***(P <0.001).
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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.