Summary
Methane emission from trees may partially or completely offset the methane sink in upland soils, the only process that has been regularly included in methane budgets for forest ecosystems. ...Our objective was to analyze multiple biogeochemical processes that influence the production, oxidation and transport of methane in a riparian cottonwood ecosystem and its adjacent river.
We combined chamber flux measurements on tree stems, forest soil and the river surface with eddy covariance measurements of methane net ecosystem exchange. In addition, we tested whether methanogens were present in cottonwood stems, shallow soil layers and alluvial groundwater.
Average midday peak in net methane emission measured by eddy covariance was c. 12 nmol m−2 s−1. The average uptake of methane by soils (0.87 nmol m−2 s−1) was largely offset by tree stem methane emission (0.75 nmol m−2 s−1). There was evidence of methanogens in tree stems but not in shallow soil.
Growing season (May–September) cumulative net methane emission (17.4 mmol CH4 m−2) included methane produced in cottonwood stems and methane input to the nocturnal boundary layer from the forest and the adjacent river. The multiple processes contributing to methane emission illustrated the linked nature of these adjacent terrestrial and aquatic ecosystems.
Abstract
Premise
Current methods for maceration of plant tissue use hazardous chemicals. The new method described here improves the safety of dissection and maceration of soft plant tissues for ...microscopic imaging by using the harmless enzyme pectinase.
Methods and Results
Leaf material from a variety of land plants was obtained from living plants and dried herbarium specimens. Concentrations of aqueous pectinase and soaking schedules were optimized, and tissues were manually dissected while submerged in fresh solution following a soaking period. Most leaves required 2–4 h of soaking; however, delicate leaves could be macerated after 30 min while tougher leaves required 12 h to 3 days of soaking. Staining techniques can also be used with this method, and permanent or semi‐permanent slides can be prepared. The epidermis, vascular tissue, and individual cells were imaged at magnifications of 10× to 400×. Only basic safety precautions were needed.
Conclusions
This pectinase method is a cost‐effective and safe way to obtain images of epidermal peels, separated tissues, or isolated cells from a wide range of plant taxa.
Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a ...two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.
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