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43 results for “enzyme function”
Molecular Models and Wave Function Definitions for Models A-G of the [2Fe]F Cluster in FeFe-hydrogenase Maturase Enzyme HydF
<p>The dataset contains all relevant atomic positional coordinates for 2Fe-cluster models, and electronic wave function data (using formatted Gaussian checkpoint files) as described in the related publication (see citation below).</p> <p>The version 2.0 contains additional models for [2Fe-2S] cluster linked [2Fe]F constructs.</p> <p>The top folder contains "analysis.xlsx" electronic spreadsheet that summarizes all the numerical results for absolute and relative electronic energy values, internal coordinates, calculated and scaled vibrational frequencies for diatomic stretching modes. The details of developing scaled quantum forcefields as a function of level of theory and model composition are also given.<br> The schematic structural definitions are given in the "models.pdf" file and keys for abbreviations are provided in "symbols.txt" file.<br> </p>
Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence
<p><i><span>Neosinocalamus affinis</span></i>, a type of cluster bamboo,<i> </i>is a good candidate feedstock for biomass energy. In the study, we found a total of 686 genes were identified as belonging to CAZyme families in the <i><span>N. affinis</span></i> transcriptome, including 222 glycoside hydrolases (GHs), 288 glycosyltransferases (GTs), 64 carbohydrate esterases (CEs), 70 auxiliary activities (AAs), 37 carbohydrate binding modules (CBMs) and five polysaccharide lyases (PLs). Expression profiles revealed that several CAZyme genes were up-regulated after insect infestation, particularly the GT, GH, AA and CE family members. Lignocellulose assays showed that the contents of three components, cellulose, hemicellulose and lignin, increased after insect infestation. Our findings showed that CAZyme genes were abundant in the <i><span>N. affinis</span></i> transcriptome and were involved in the response to herbivory. These findings could be applied to protect bamboo against herbivores, such as the bamboo snout beetle <i><span>Cyrtotrachelus buqueti</span></i>, and develop low-cost chemical feedstock from bamboo.</p>
Data from: Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies
Mating behaviours are diverse and noteworthy, especially within species radiations where they may contribute to speciation. Studying how differences in mating behaviours arise between species can help us understand how diversity is generated at multiple biological levels. The bioluminescent courtship displays of cypridinid ostracods (or sea fireflies) are an excellent system for this since amazing variety evolves while using a conserved biochemical mechanism. We find that the evolution of one aspect in this behavioural phenotype - the duration of bioluminescent courtship pulses - is shaped by biochemical function. First, by measuring light production from induced bioluminescence in 38 species, we discovered differences between species in their biochemical reactions. Then, for 16 species of which biochemical, phylogenetic, and behavioral data are all available, we used phylogenetic comparative models to show that differences in biochemical reaction are nonlinearly correlated with the duration of courtship pulses. This relationship indicates that changes to both enzyme (c-luciferase) function and usage have shaped the evolution of courtship displays, but that they differentially contribute to these phenotypic changes. This nonlinear dynamic may have consequences for the disparity of signaling phenotypes observed across species, and demonstrates how unappreciated diversity at the biochemical level can lead to inferences about behavioural evolution.
Data and metadata of soil microbial community structure, enzyme activities, functional genes and earthworms derived from H2020 Diverfarming project
<p>Soil data and metadata of soil microbial community structure, enzyme activities (dehydrogenase, β-glucosidase, leucine-aminopeptidase, alkaline phosphatase and arylsusfatase activities), N functional genes and earthworms from the different cases studies and long terms from WP4 "Impact of crop diversification on biodiversity", derived from H2020 Diverfarming project. The main objective of workpackage is to provide a scientific understanding of the link between diversified cropping systems, above- and belowground biodiversity, and the resulting ecosystem services provided by soil microorganisms, soil invertebrates and vegetation in agro-ecosystems. Soil organisms contribute to all biogeochemical cycles, Soil organic matter mineralization and stabilization, shape soil structure and have associations with plant species promoting growth and development. http://www.diverfarming.eu.</p>
Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia
<p class="MsoNormal"><span>These data were generated to investigate the association and functional analysis of angiotensin-converting enzyme 2 genetic variants with the pathogenesis of pre-eclampsia(PE). This study conducted a case-control study involving 327 PE patients and 591 healthy pregnant women to explore the associations between candidate variants in the ACE2 gene variants and the pathogenesis of PE.This study collected clinical samples and data, and used logistic regression, false positive report rate, multi factor dimension reduction, functional analysis and other analysis methods to process the research data. </span>Potential functional ACE2 gene variants (rs2106809 A>G, rs6632677 G>C, and rs2074192 C>T) were selected and genotyped using kompetitive allele-specific PCR. The strength of the associations between the studied genetic variants and the risk of PE were evaluated using odds ratios (ORs) and corresponding 95% confidence intervals (CIs).<span> Finally,it showed that the rs2106809 A>Gis significantly associated with the risk of PE via individual locus effects and/or complex gene-gene and gene-environment interactions.</span><span> </span></p>
Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence
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Data from: Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies
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Comparative functional analyses of the prostate-specific KLK3 enzyme in primates reveal the impact of sexual selection
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Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia
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Soil microbial functions and enzyme activity:BAC: Biodiversity and Climate
Climate changes forecast for our region by GCM???s and shifts in biodiversity and composition each have the potential to alter ecosystem functioning; their interactive effects are unknown. The "BAC" experiment is designed to determine the direct and interactive effects of plant species numbers, plant community composition, temperature, and precipitation on 11 productivity, C and N dynamics, stability, and plant, microbe, and insect species abundances in CDR grassland ecosystems.
Convergence in Determining Enzyme Functional Descriptors across Kemp Eliminase Variants
<p>SI data for the paper with the same title: Initial topology and coordinate files for 18 KE07-R7-2.</p>
Comparison of Standard Versus Low Dose Advagraf® With or Without Angiotensin-converting Enzyme Inhibitor (ACEi)/Angiotensin Receptor Blocker (ARB) on Histology and Function of Renal Allografts
ClinicalTrials.gov study NCT00933231. IPD Sharing: NO. Countries: 1. Publications: 3.
Unrecognized controls on microbial functioning in Blue Carbon ecosystems: the role of mineral enzyme stabilization and allochthonous substrate supply
Tidal wetlands are effective carbon sinks, mitigating climate change through the long-term removal of atmospheric CO2. Studies along surface-elevation and thus flooding-frequency gradients in tidal wetlands are often used to understand the effects of accelerated sea-level rise on carbon sequestration, a process that is primarily determined by the balance of primary production and microbial decomposition. It has often been hypothesized that rates of microbial decomposition would increase with elevation and associated increases in soil oxygen availability; however, previous studies yield a wide range of outcomes and equivocal results. Our mechanistic understanding of the elevation-decomposition relationship is limited because most effort has been devoted to understanding the terminal steps of the decomposition process. Few studies assessed microbial exo-enzyme activities (EEAs) as initial and rate-limiting steps that often reveal important insight into microbial energy and nutrient constraints. The present study assessed EEAs and microbial abundance along a coastal ecotone stretching a flooding gradient from tidal flat to high marsh in the European Wadden Sea. We found that stabilization of exo-enzymes to mineral sediments leads to high specific EEAs at low substrate concentrations in frequently flooded, sediment rich zones of the studied ecotone. We argue that the high background activity of a mineral-associated enzyme pool provides a stable decomposition matrix in highly dynamic, frequently flooded zones. Furthermore, we demonstrate that microbial communities are less nutrient limited in frequently flooded zones, where inputs of nutrient-rich marine organic matter are higher. This was reflected in both increasing exo-enzymatic carbon-vs.-nutrient acquisition and decreasing fungal-vs.-bacterial abundance with increasing flooding frequency. Our findings thereby suggest two previously unrecognized mechanisms that may contribute to stimulated microbial activity despite decreasing oxygen availability in response to accelerated sea-level rise.
Pancreatic Enzymes to Restore Digestive Function in Malnourished Gastric Bypass Patients
ClinicalTrials.gov study NCT00510744. IPD Sharing: YES. Countries: 1. Publications: 0.
L-Arginine Supplementation With or Without Enzyme Inhibitors Treating Erectile Function of Prostate Cancer Survivors
ClinicalTrials.gov study NCT01105130. IPD Sharing: NO. Countries: 1. Publications: 0.
Unrecognized controls on microbial functioning in Blue Carbon ecosystems: the role of mineral enzyme stabilization and allochthonous substrate supply
Open the record for dataset details and reuse information.
Single-cell RNA-sequencing data and functional analysis revealed that ACC1, a rate limiting enzyme of fatty acid biosynthesis, is responsible for survival of thymic iNKT cells.
GEO Series GSE248939. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide Nicking Enzyme Epitope targeted DNA sequencing.
GEO Series GSE261834. Homo sapiens. 51 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Transforming growth factor β/activin signaling functions as a sugar-sensing feedback loop to regulate digestive enzyme expression.
GEO Series GSE54755. Drosophila melanogaster. 9 samples. Type: Expression profiling by high throughput sequencing.
Discovery of novel hyperthermophilic DNA modifying enzymes using a functional genomics screen
GEO Series GSE182067. Thermococcus kodakarensis. 1 samples. Type: Expression profiling by high throughput sequencing.
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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.