A computational model of finite-length undulatory swimmers is used to examine the physical origin of the effect of elasticity on swimming speed. We explore two distinct target swimming strokes: one ...derived from the motion of Caenorhabditis elegans, with large head undulations, and a contrasting stroke with large tail undulations. We show that both favorable stroke asymmetry and swimmer elasticity contribute to a speed-up, but a substantial boost results only when these two effects work together. We reproduce conflicting results from the literature simply by changing relevant physical parameters.
Plant growth–promoting bacteria show great potential for use in agriculture although efficient application remains challenging to achieve. Cells often lose viability during inoculant production and ...application, jeopardizing the efficacy of the inoculant. Since desiccation has been documented to be the primary stress factor affecting the decrease in survival, obtaining xerotolerance in plant growth–promoting bacteria is appealing. The molecular damage that occurs by drying bacteria has been broadly investigated, although a complete view is still lacking due to the complex nature of the process. Mechanic, structural, and metabolic changes that occur as a result of water depletion may potentially afflict lethal damage to membranes, DNA, and proteins. Bacteria respond to these harsh conditions by increasing production of exopolysaccharides, changing composition of the membrane, improving the stability of proteins, reducing oxidative stress, and repairing DNA damage. This review provides insight into the complex nature of desiccation stress in bacteria in order to facilitate strategic choices to improve survival and shelf life of newly developed inoculants.
Key Points
Desiccation-induced damage affects most major macromolecules in bacteria.
Most bacteria are not xerotolerant despite multiple endogenous adaption mechanisms.
Sensitivity to drying severely hampers inoculant quality.
Blebs are pressure-driven protrusions that play an important role in cell migration, particularly in three-dimensional environments. A bleb is initiated when the cytoskeleton detaches from the cell ...membrane, resulting in the pressure-driven flow of cytosol toward the area of detachment and local expansion of the cell membrane. Recent experiments involving blebbing cells have led to conflicting hypotheses regarding the timescale of intracellular pressure propagation. The interpretation of one set of experiments supports a poroelastic model of the cytoplasm that leads to slow pressure equilibration when compared to the timescale of bleb expansion. A different study concludes that pressure equilibrates faster than the timescale of bleb expansion. To address this discrepancy, a dynamic computational model of the cell was developed that includes mechanics of and the interactions among the cytoplasm, the actin cortex, the cell membrane, and the cytoskeleton. The model results quantify the relationship among cytoplasmic rheology, pressure, and bleb expansion dynamics, and provide a more detailed picture of intracellular pressure dynamics. This study shows the elastic response of the cytoplasm relieves pressure and limits bleb size, and that both permeability and elasticity of the cytoplasm determine bleb expansion time. Our model with a poroelastic cytoplasm shows that pressure disturbances from bleb initiation propagate faster than the timescale of bleb expansion and that pressure equilibrates slower than the timescale of bleb expansion. The multiple timescales in intracellular pressure dynamics explain the apparent discrepancy in the interpretation of experimental results.
In Populus trichocarpa (black cottonwood), net photosynthesis (An) varies with latitude and, in northern genotypes, is supported by higher stomatal conductance (gs). We report here a parallel cline ...in mesophyll conductance (gm) and link this variation to carbonic anhydrase (CA) activity. Using concurrent carbon isotope discrimination and chlorophyll fluorescence methods, we examined the effects of acetazolamide, an inhibitor of CA, on gm in six representative genotypes (three from either end of the north‐south cline). Acetazolamide reduced CA activity, gm, gs, chloroplast CO2 concentration (Cc) and An at normal CO2 (400 μmol mol−1), the latter being reversible at saturating CO2. Absolute reductions in An, gm and CA activity were greater in northern genotypes than in southern genotypes (P < 0.025) but percent reductions were similar. In contrast, northern genotypes showed lower percent reduction in Cc compared to southern genotypes (P < 0.025). The northern genotypes had greater CA activity relative to both leaf area (two‐fold) and mass (1.8‐fold) (P < 0.016). The relationship between CA activity and gm was similar whether the variation was inherent or inhibitor induced. We suggest that greater CA activity contributes to higher gm in northern P. trichocarpa genotypes, but other diffusion pathway components may also be involved.
Using chlorophyll fluorescence and isotope discrimination methods, we demonstrate that higher photosynthetic rates in black cottonwood accessions originating from higher latitude are partially supported by higher mesophyll conductance. High latitude genotypes had higher carbonic anhydrase activity and showed less reduction in chloroplast CO2 concentrations when treated with acetazolamide, an inhibitor of carbonic anhydrase. Natural and inhibitor‐induced variations in carbonic anhydrase activity were similarly well correlated with mesophyll conductance.
Questions
Do nitrogen deposition and climate warming affect tree seedlings and plant communities in different habitats? In these habitats, how do microenvironments, including soil properties and, ...when applicable, edge effects relate to plant performance?
Location
The University of British Columbia Malcolm Knapp Research Forest, Maple Ridge, British Columbia, Canada.
Methods
We assessed performance of Pseudotsuga menziesii (Mirb.) Franco, Thuja plicata Donn ex D. Don and Tsuga heterophylla (Raf.) Sarg. planted tree seedlings and associated vascular plant communities. Performance of tree seedlings (height) and under vascular plant communities (percent cover) were examined in an experiment with warming (open‐top chambers) and nitrogen deposition (ammonium nitrate applied at 10 kg N ha−1 year−1) treatments applied to subplots in six forest edges and six clear‐cuts (N = 298 total subplots).
Results
In clear‐cuts, tree seedling height increased with experimental warming and differed among species, and vascular plant cover increased with warming. In clear‐cuts, species identity, not soil variables, was a strong predictor of height, and plant cover was negatively related to pH. In forest edges, edge position and some soil variables were related to height, but not plant cover. There were no interaction effects found between experimental nitrogen deposition and warming.
Conclusions
Our results suggest that moderate warming can enhance tree seedling height and understorey vascular plant cover in clear‐cuts in Pacific Northwest coastal ecosystems, but low nitrogen deposition may not have an effect alone or synergistically with warming.
With a field experiment, we studied nitrogen deposition and climate warming impacts on planted tree seedlings and associated understory plants in clear‐cuts and forest edges. Microenvironments were assessed, including soil properties and edge effects. Microenvironmental effects on plants were habitat dependent. Moderate climate warming may enhance tree seedling performance and plant cover in a clear‐cuts of Pacific Northwest coastal ecosystems.
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet it only achieves first-order spatial accuracy near embedded boundaries. In ...this paper, we introduce a new high-order numerical method which we call the Immersed Boundary Smooth Extension (IBSE) method. The IBSE method achieves high-order accuracy by smoothly extending the unknown solution of the PDE from a given smooth domain to a larger computational domain, enabling the use of simple Cartesian-grid discretizations (e.g. Fourier spectral methods). The method preserves much of the flexibility and robustness of the original IB method. In particular, it requires minimal geometric information to describe the boundary and relies only on convolution with regularized delta-functions to communicate information between the computational grid and the boundary. We present a fast algorithm for solving elliptic equations, which forms the basis for simple, high-order implicit-time methods for parabolic PDE and implicit–explicit methods for related nonlinear PDE. We apply the IBSE method to solve the Poisson, heat, Burgers', and Fitzhugh–Nagumo equations, and demonstrate fourth-order pointwise convergence for Dirichlet problems and third-order pointwise convergence for Neumann problems.
Summary
Carbonic anhydrase (CA) is an abundant protein in most photosynthesizing organisms and higher plants. This review paper considers the physiological importance of the more abundant CA isoforms ...in photosynthesis, through their effects on CO2 diffusion and other processes in photosynthetic organisms. In plants, CA has multiple isoforms in three different families (α, β and γ) and is mainly known to catalyze the CO2 ↔ HCO3- equilibrium. This reversible conversion has a clear role in photosynthesis, primarily through sustaining the CO2 concentration at the site of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco). Despite showing the same major reaction mechanism, the three main CA families are evolutionarily distinct. For different CA isoforms, cellular localization and total gene expression as a function of developmental stage are predicted to determine the role of each family in relation to the net assimilation rate. Reaction–diffusion modeling and observational evidence support a role for CA activity in reducing resistance to CO2 diffusion inside mesophyll cells by facilitating CO2 transfer in both gas and liquid phases. In addition, physical and/or biochemical interactions between CAs and other membrane‐bound compartments, for example aquaporins, are suggested to trigger a CO2‐sensing response by stomatal movement. In response to environmental stresses, changes in the expression level of CAs and/or stimulated deactivation of CAs may correspond with lower photosynthetic capacity. We suggest that further studies should focus on the dynamics of the relationship between the activity of CAs (with different subcellular localization, abundance and gene expression) and limitations due to CO2 diffusivity through the mesophyll and supply of CO2 to photosynthetic reactions.
Significance Statement
This review considers the physiological importance of the more abundant carbonic anhydrase (CA) isoforms in photosynthesis through their effects on CO2 diffusion and other processes. We suggest that future studies should focus on the dynamics of the relationship between the activity of various CAs and limitations due to CO2 diffusivity through the mesophyll and supply of CO2 to photosynthetic reactions.
The role of passive body dynamics on the kinematics of swimming micro-organisms in complex fluids is investigated. Asymptotic analysis of small-amplitude motions of a finite-length undulatory swimmer ...in a Stokes–Oldroyd-B fluid is used to predict shape changes that result as body elasticity and fluid elasticity are varied. Results from the analysis are compared with numerical simulations and the numerically simulated shape changes agree with the analysis at both small and large amplitudes, even for strongly elastic flows. We compute a stroke-induced swimming speed that accounts for the shape changes, but not additional effects of fluid elasticity. Elasticity-induced shape changes lead to larger-amplitude strokes for sufficiently soft swimmers in a viscoelastic fluid, and these stroke boosts can lead to swimming speed-ups. However, for the strokes we examine, we find that additional effects of fluid elasticity generically result in a slow-down. Our high amplitude strokes in strongly elastic flows lead to a qualitatively different regime in which highly concentrated elastic stresses accumulate near swimmer bodies and dramatic slow-downs are seen.
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet for fluid problems it only achieves first-order spatial accuracy near embedded ...boundaries for the velocity field and fails to converge pointwise for elements of the stress tensor. In a previous work we introduced the Immersed Boundary Smooth Extension (IBSE) method, a variation of the IB method that achieves high-order accuracy for elliptic PDE by smoothly extending the unknown solution of the PDE from a given smooth domain to a larger computational domain, enabling the use of simple Cartesian-grid discretizations. In this work, we extend the IBSE method to allow for the imposition of a divergence constraint, and demonstrate high-order convergence for the Stokes and incompressible Navier–Stokes equations: up to third-order pointwise convergence for the velocity field, and second-order pointwise convergence for all elements of the stress tensor. The method is flexible to the underlying discretization: we demonstrate solutions produced using both a Fourier spectral discretization and a standard second-order finite-difference discretization.
After root uptake, nitrate is effluxed back to the medium, assimilated locally, or translocated to shoots. Rooted black cottonwood (Populus trichocarpa) scions were supplied with a NO3−‐based (0.5 ...mM) nutrient medium of known isotopic composition (δ15N), and xylem sap was collected by pressure bombing. To establish a sampling protocol, sap was collected from lower and upper stem sections at 0.1–0.2 MPa above the balancing pressure, and after increasing the pressure by a further 0.5 MPa. Xylem sap from upper stem sections was partially diluted at higher pressure. Further analysis was restricted to sap obtained from intact shoots at low pressure. Total‐, NO3−‐N and, by difference, organic‐N concentrations ranged from 6.1–11.0, 1.2–2.4, and 4.6–9.4 mM, while discrimination relative to the nutrient medium was −6.3 to 0.5‰, −23.3 to −11.5‰ and − 1.3 to 4.9‰, respectively. There was diurnal variation in δ15N of total‐ and organic‐N, but not NO3−. The difference in δ15N between xylem NO3− and organic‐N suggests that discrimination by nitrate reductase is near 25.1 ± 1.6‰. When this value was used in an isotope mass balance model, the predicted xylem sap NO3−‐N to total‐N ratio closely matched direct measurement.
The bulk nitrogen stable isotopic composition of xylem should reflect contributions from isotopically lighter assimilated nitrogen and isotopically heavier inorganic nitrogen. Xylem water expressed from stems of black cottonwood (Populus trichocarpa) supplied with 0.5 mM NO3−had bulk, organic, and inorganic N concentrations ranging from 6.1–11.0, 4.6–9.4, and 1.2–2.4 mM, respectively. Discrimination relative to the hydroponic source was −6.3 to 0.5‰, −1.3 to 4.9‰ and − 23.3 to −11.5‰, respectively. The average difference in δ15N between xylem NO3− and organic N suggests an in vivo discrimination factor for nitrate assimilation of 25.1‰.
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