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1,204 results for “Enzymes”
Data from: Polybrominated diphenyl ether (DE-71) exposure skews phenotypic sex ratio, and alters steroid hormone levels and steroidogenic enzyme activities in juvenile Silurana tropicalis
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Data from: Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry
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Imprint of tree species mycorrhizal association on microbial-mediated enzyme activity and stoichiometry
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Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure
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Data for: The galactokinase enzyme of yeast senses metabolic flux to stabilize GAL pathway regulation
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Data from: Biosynthesis of the redox coenzyme F420 in Thermomicrobia involves reduction by standalone nitroreductase superfamily enzymes.
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Preliminary phylogenetic and plasmid data for microbial laccase, fluorinase, dehalogenase, and glycyl radical enzymes
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Extracellular enzyme: Effects of Nitrogen Fertilization on Litter and Soil Decomposition
The influence of inorganic nitrogen (N) inputs on decomposition is poorly understood. Some prior studies suggest that N may reduce the decomposition of substrates with high concentrations of lignin via inhibitory effects on the activity of lignin-degrading enzymes, although such inhibition has not always been demonstrated. The purpose of E145 was to study the effects of nitrogen (N) addition on decomposition of seven substrates ranging in initial lignin concentrations (from 7.4 - 25.6%) over five years in eight different grassland and forest sites in central Minnesota.
Substrate mass, nitrogen, extracellular enzyme, and microbial biomass and stoichiometry dynamics: Nitrogen limitation in decomposition
Modern agriculture and fossil fuel combustion contribute to the transfer of N from largely inert pools (atmospheric N2, fossil fuel reserves) to biologically reactive forms that can be transported downwind from agricultural or industrial areas to ecosystems that historically may have experienced low levels of N inputs. Understanding how increased N inputs alter the cycling of another biologically important element, C, has been impeded by uncertainties about N effects on the process of decomposition. To date, ecologists remain unable to predict when, where, and in what forms N addition stimulates rates of decomposition. For example, recent work showed that in eight low-N sites in Central Minnesota, litter N was positively correlated with decomposition, suggesting N limitation of decomposition, yet addition of inorganic N fertilizer increased decomposition in only two of eight sites. These paradoxical results call into question the assumption that the often-observed correlation between substrate N concentration and decomposition arises because N limits decomposition. Research is addressing three interrelated questions:* (1) Why do litter N and externally supplied N have contrasting effects on decomposition in low-N ecosystems? (2) Do different forms of N (organic vs. inorganic; substrate vs. externally supplied) affect the activity, function and composition of the decomposer community differently, and, if so, what are the consequences for decomposition? (3) What are temporal dynamics of the activity, function, and composition of the decomposer community and do these dynamics depend upon the amount and forms of N supplied to the decomposer community?* These questions will be addressed using a 4-y decomposition experiment manipulating the quantity and form of N available to decomposers via use of substrates ranging in N concentrations and of inorganic (ammonium nitrate) and organic (amino acids) N fertilizers. The response of microbial biomass, stoichiometry, efficiency
O horizon extracellular enzyme activity: Nitrogen limitation in decomposition
Modern agriculture and fossil fuel combustion contribute to the transfer of N from largely inert pools (atmospheric N2, fossil fuel reserves) to biologically reactive forms that can be transported downwind from agricultural or industrial areas to ecosystems that historically may have experienced low levels of N inputs. Understanding how increased N inputs alter the cycling of another biologically important element, C, has been impeded by uncertainties about N effects on the process of decomposition. To date, ecologists remain unable to predict when, where, and in what forms N addition stimulates rates of decomposition. For example, recent work showed that in eight low-N sites in Central Minnesota, litter N was positively correlated with decomposition, suggesting N limitation of decomposition, yet addition of inorganic N fertilizer increased decomposition in only two of eight sites. These paradoxical results call into question the assumption that the often-observed correlation between substrate N concentration and decomposition arises because N limits decomposition. Research is addressing three interrelated questions:* (1) Why do litter N and externally supplied N have contrasting effects on decomposition in low-N ecosystems? (2) Do different forms of N (organic vs. inorganic; substrate vs. externally supplied) affect the activity, function and composition of the decomposer community differently, and, if so, what are the consequences for decomposition? (3) What are temporal dynamics of the activity, function, and composition of the decomposer community and do these dynamics depend upon the amount and forms of N supplied to the decomposer community?* These questions will be addressed using a 4-y decomposition experiment manipulating the quantity and form of N available to decomposers via use of substrates ranging in N concentrations and of inorganic (ammonium nitrate) and organic (amino acids) N fertilizers. The response of microbial biomass, stoichiometry, efficiency
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.
Data from: Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids
<p>Chiococca alba (L.) Hitchc. (snowberry), a member of the Rubiaceae, has been used as a folk remedy for a range of health issues including inflammation and rheumatism and produces a wealth of specialized metabolites including terpenes, alkaloids, and flavonoids. We generated a 558 Mb draft genome assembly for snowberry which encodes 28,707 high confidence genes. Comparative analyses with other angiosperm genomes revealed enrichment in snowberry of lineage-specific genes involved in specialized metabolism. Synteny between snowberry and Coffea canepehora Pierre ex A. Froehner (coffee) was evident, including the chromosomal region encoding caffeine biosynthesis in coffee, albeit syntelogs of N-methyltransferase were absent in snowberry. A total of 27 putative terpene synthase genes were identified, including 10 that encode diterpene synthases. Functional validation of a subset of putative terpene synthases revealed that combinations of diterpene synthases yielded access to products of both general and specialized metabolism. Specifically, we identified plausible intermediates in the biosynthesis of merilactone and ribenone, structurally unique antimicrobial diterpene natural products. Access to the C. alba genome will enable additional characterization of biosynthetic pathways responsible for health-promoting compounds in this medicinal species.</p>
Plasmid Design for Tunable Two‐Enzyme Co‐Expression Promotes Whole‐Cell Production of Cellobiose
<p>We provide underlying data for the publication "Plasmid design for tunable two-enzyme co-expression promotes whole-cell production of cellobiose". Please find the abstract below.</p> <p>Catalyst development for biochemical cascade reactions often follows a “whole cell approach” in which a single microbial cell is made to express all of the required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux from substrate to product necessitates precise balancing between the individual activities. Here, we show effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors enabling tunable two‐enzyme co‐expression in <em>E. coli </em>, for the purpose of whole‐cell production of cellobiose. Flux efficiency in the transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co‐expression cope with large differences in the specific activity of cellobiose phosphorylase (14 U mg<sup>−1</sup>) and sucrose phosphorylase (122 U mg<sup>−1</sup>). Comparing mono‐ and bicistronic co‐expression strategies, we analyze genetic elements controlling transcription, transcription‐translation coupling or plasmid replication for effect on activity, and also stable producibility, of the whole cell catalyst. We discover a key role of the <em>bom </em>(basis of mobility) site for plasmid stability dependent on the origin of replication and demonstrate the importance of RBS (ribosome binding site) strength for balanced bicistronic co‐expression. Whole cell catalysts show high specific rates (460 μmol cellobiose min<sup>−1</sup> g<sup>−1</sup> dry cells) and performance metrics (30 g L<sup>−1</sup>; ∼82% yield; 3.8 g L<sup>−1</sup> h<sup>−1</sup> overall productivity) promising for cellobiose production.</p>
The Alginate Immobilization of Metabolic Enzymes (AIME) platform retrofits an estrogen receptor transactivation assay with metabolic competence
The U.S. EPA Endocrine Disruptor Screening Program utilizes data across the ToxCast/Tox21 high-throughput screening (HTS) programs to evaluate the biological effects of potential endocrine active substances (EAS). A potential limitation to the use of in vitro assay data in regulatory decision-making is the lack of coverage for xenobiotic metabolic processes. Both hepatic- and peripheral-tissue metabolism can yield metabolites that exhibit greater activity than the parent compound (bioactivation) or are inactive (bioinactivation) for a given biological target. Interpretation of biological effect data for both putative EAS, as well as other chemicals, screened in HTS assays may benefit from the addition of xenobiotic metabolic capabilities to decrease the uncertainty in predicting potential hazards to human health. The objective of this study was to develop an approach to retrofit existing HTS assays with hepatic metabolism. The Alginate Immobilization of Metabolic Enzymes (AIME) platform encapsulates hepatic S9 fractions in alginate microspheres attached to 96-well peg lids. Functional characterization across a panel of reference substrates for phase I cytochrome P450 enzymes revealed substrate depletion with expected metabolite accumulation. Performance of the AIME method in the VM7Luc estrogen receptor (ER) transactivation assay was evaluated across 15 reference chemicals and 48 test chemicals that yield metabolites previously identified as ER active or inactive. The results demonstrate the utility of applying the AIME method for identification of false positive and false negative target assay effects, reprioritization of hazard based on metabolism-dependent bioactivity, and enhanced in vivo concordance with the rodent uterotrophic bioassay. Integration of the AIME metabolism method may prove useful for future biochemical and cell-based HTS applications.
Parallel molecular mechanisms for enzyme temperature adaptation
<p><span>The mechanisms that underly the adaptation enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Herein, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis</span><span> and we establish the underlying physical mechanisms</span><span>. </span>This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature in 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation. We assess the properties of these residues, molecular interactions and interaction networks that appear to underly temperature adaptation.</p>
Data from: Changes in levels of enzymes and osmotic adjustment compounds in key species and their relevance to vegetation succession in abandoned croplands of a semiarid sandy region
<p>Reclamation of cropland from grassland is regarded as a main reason for grassland degradation; understanding succession from abandoned cropland to grassland is thus crucial for vegetation restoration in arid and semiarid areas. Soil becomes dry when cropland is reverted to grassland, and enzyme and osmotic adjustment compounds may help plants to adapt to a drying environment. Croplands that were abandoned in various years on the Ordos Plateau in China, were selected for the analysis of the dynamics of enzymes and osmotic adjustment compounds in plant species during vegetation succession. With increasing number of years since abandonment, levels of superoxide dismutase<span> increased</span><span> in </span><i><span><span>Stipa</span></span></i><i><span><span> bungeana</span></span></i><span>, first decreased </span><span>and then increased in </span><i><span><span>Lespedeza</span></span></i><i><span><span> davurica</span></span></i><span> and </span><i><span><span>Artemisia f</span></span></i><i><span><span>rigida</span></span></i><span>, and fluctuated in </span><i><span><span>Heteropappus altaicus</span></span></i><span>. Levels</span> of<span> peroxidase and catalase in the four species fluctuated</span><span>;</span> levels of<span> proline, soluble sugar and soluble protein either</span><i> </i><span>decreas</span><span>ed</span><span> or</span><span> first </span><span>increase</span><span>d</span><span> and</span><span> then</span><span> generally decreased.</span> According to <span>a </span><span>drought resistance</span><span> index</span>, the <span>drought resistance of the </span><span>four </span><span>species</span><span> was </span><span>ranked in descending order as follows</span>: <i><span>S. bungeana </span></i><span>> </span><i><span>A. frigida </span></i><span>> </span><i><span>H. altaicus</span></i> <span>> </span><i><span>L. davurica</span></i>. The drought resistance ability of the different species was<span> closely linked with vegetation succession from communities dominated by annual and biennial species (with main accompanying species of </span><i><span><span>L.</span></span></i><i><span><span> davurica</span></span></i> <span>and</span><i><span><span> H. altaicus</span></span></i><span>) to communities dominated by perennial species (</span><i><span><span>S.</span></span></i><i><span><span> bungeana</span></span></i><span> and </span><i><span><span>A. f</span></span></i><i><span><span>rigida</span></span></i><span>) when soil became dry owing to increasing evapotranspiration after cropland abandonment. </span>The restoration of <i><span>S. bungeana </span></i>steppe after cropland abandonment on the Ordos Plateau<span> is recommended both as high-quality forage and for environmental sustainability</span>.</p>
Quadriceps muscle power and optimal shortening velocity are inversely related to angiotensin converting enzyme activity in older men
<p>This dataset corresponds to the article titled "Quadriceps muscle power and optimal shortening velocity are inversely related to angiotensin converting enzyme activity in older men"</p>
Drosophila carboxypeptidase D (SILVER) is a key enzyme in neuropeptide processing required to maintain locomotor activity levels and survival rate
<p>Neuropeptides are processed from larger preproproteins by a dedicated set of enzymes. The molecular and biochemical mechanisms underlying preproprotein processing and the functional importance of processing enzymes are well‐characterised in mammals, but little studied outside this group. In contrast to mammals, Drosophila melanogaster lacks a gene for carboxypeptidase E (CPE), a key enzyme for mammalian peptide processing. By combining peptidomics and neurogenetics, we addressed the role of carboxypeptidase D (dCPD) in global neuropeptide processing and selected peptide‐regulated behaviours in Drosophila. We found that a deficiency in dCPD results in C‐terminally extended peptides across the peptidome, suggesting that dCPD took over CPE function in the fruit fly. dCPD is widely expressed throughout the nervous system, including peptidergic neurons in the mushroom body and neuroendocrine cells expressing adipokinetic hormone. Conditional hypomorphic mutation in the dCPD‐encoding gene silver in the larva causes lethality, and leads to deficits in starvation‐induced hyperactivity and appetitive gustatory preference, as well as to reduced viability and activity levels in adults. A phylogenomic analysis suggests that loss of CPE is not common to insects, but only occurred in Hymenoptera and Diptera. Our results show that dCPD is a key enzyme for neuropeptide processing and peptide‐regulated behaviour in Drosophila. dCPD thus appears as a suitable target to genetically shut down total neuropeptide production in peptidergic neurons. The persistent occurrence of CPD in insect genomes may point to important further CPD functions beyond neuropeptide processing which cannot be fulfilled by CPE.</p>
Data from: Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion
A kinetic model combining enzyme activity measurements and subcellular compartmentation was parameterized to fit the sucrose, hexose, and glucose-6-P contents of pericarp throughout tomato (Solanum lycopersicum) fruit development. The model was further validated using independent data obtained from domesticated and wild tomato species and on transgenic lines. A hierarchical clustering analysis of the calculated fluxes and enzyme capacities together revealed stage-dependent features. Cell division was characterized by a high sucrolytic activity of the vacuole, whereas sucrose cleavage during expansion was sustained by both sucrose synthase and neutral invertase, associated with minimal futile cycling. Most importantly, a tight correlation between flux rate and enzyme capacity was found for fructokinase and PPi-dependent phosphofructokinase during cell division and for sucrose synthase, UDP-glucopyrophosphorylase, and phosphoglucomutase during expansion, thus suggesting an adaptation of enzyme abundance to metabolic needs. In contrast, for most enzymes, flux rates varied irrespectively of enzyme capacities, and most enzymes functioned at <5% of their maximal catalytic capacity. One of the major findings with the model was the high accumulation of soluble sugars within the vacuole together with organic acids, thus enabling the osmotic-driven vacuole expansion that was found during cell division.
Data from: Overexpression of an antioxidant enzyme improves male mating performance after stress in a lek-mating fruit fly
In many species, courtship displays are reliable signals of male quality, and current hypotheses suggest that mitochondrial function is a key mechanism underlying these condition-dependent traits. Environmental stressors generate reactive oxygen species (ROS) that impair mitochondrial function, and thus antioxidant pathways that remove ROS are likely critical for preserving complex sexual behaviors. Here, we test the hypothesis that enhanced antioxidant activity in mitochondria preserves mating performance following oxidative stress. Using a transgenic approach, we directly manipulated mitochondrial antioxidant activity in the Caribbean fruit fly, Anastrepha suspensa, a lek-mating species with elaborate sexual displays and intense sexual selection that is also a model for Sterile Insect Technique programs. We generated seven transgenic lines that overexpress mitochondrial superoxide dismutase (MnSOD). Radiation is a severe oxidative stressor used commonly to induce sterility for sterile insect programs. After radiation treatment, two lines with intermediate MnSOD overexpression showed enhanced mating performance relative to wild-type males. These improvements in mating corresponded with reduced oxidative damage to lipids, demonstrating that MnSOD overexpression protects flies from oxidative stress at the cellular level. For lines with improved mating performance, overexpression also preserved locomotor activity, as indicated by a laboratory climbing assay. Our results show a clear link between oxidative stress, antioxidant capacity, and male performance. Our work has implications both for fundamentally understanding the role of mitochondrial antioxidants in sexual selection and shows promise for using transgenic approaches to enhance the field performance of insects released for area-wide pest management strategies and improving performance of biological control agents in general.
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Allen Brain Atlas
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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.
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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.
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