Nitrogen inputs best predict farm field nitrate leaching in the Willamette Valley, Oregon.

Nitrate leaching is an important yet difficult to manage contribution to groundwater and surface water contamination in agricultural areas. We examine 14 farm fields over a four year period (2014-2017) in the southern Willamette Valley, providing 53 sets of annual, field-level agricultural performance metrics related to nitrogen (N), including fertilizer inputs, crop harvest outputs, N use efficiency (NUE), nitrate-N leaching and surplus N. Crop-specific nitrate-N leaching varied widely from 10 kg N ha-1yr-1 in hazelnuts to >200 kg N ha-1yr-1 in peppermint. Averaging across all sites and years, most leaching occurred during fall (60%) and winter (32%). Overall NUE was 57%. We used a graphical approach to explore the relationships between N inputs, surplus, crop N harvest removal and NUE by crop type. The blueberry site had high inputs and surplus, peppermint had high inputs but also high crop N removal and NUE and thus lower surplus, and most wheat crops had high NUE and evidence of using soil N. Annual N surplus was not well correlated with leaching, and leaching varied more by crop type and inputs. Grass seed and hazelnuts, which are dominant crop types in the southern Willamette Valley, were intermediate in terms of NUE, leaching and surplus. Of all performance metrics, N input was most closely aligned with field-level crop N harvest and nitrate leaching, therefore optimizing N inputs may well inform local efforts to reduce groundwater nitrate contamination.

An architectural understanding of natural sway frequencies in trees.

The relationship between form and function in trees is the subject of a longstanding debate in forest ecology and provides the basis for theories concerning forest ecosystem structure and metabolism. Trees interact with the wind in a dynamic manner and exhibit natural sway frequencies and damping processes that are important in understanding wind damage. Tree-wind dynamics are related to tree architecture, but this relationship is not well understood. We present a comprehensive view of natural sway frequencies in trees by compiling a dataset of field measurement spanning conifers and broadleaves, tropical and temperate forests. The field data show that a cantilever beam approximation adequately predicts the fundamental frequency of conifers, but not that of broadleaf trees. We also use structurally detailed tree dynamics simulations to test fundamental assumptions underpinning models of natural frequencies in trees. We model the dynamic properties of greater than 1000 trees using a finite-element approach based on accurate three-dimensional model trees derived from terrestrial laser scanning data. We show that (1) residual variation, the variation not explained by the cantilever beam approximation, in fundamental frequencies of broadleaf trees is driven by their architecture; (2) slender trees behave like a simple pendulum, with a single natural frequency dominating their motion, which makes them vulnerable to wind damage and (3) the presence of leaves decreases both the fundamental frequency and the damping ratio. These findings demonstrate the value of new three-dimensional measurements for understanding wind impacts on trees and suggest new directions for improving our understanding of tree dynamics from conifer plantations to natural forests.

Noninvasive quantitative measurement of bacterial growth in porous media under unsaturated-flow conditions.

Glucose-dependent growth of the luxCDABE reporter bacterium Pseudomonas fluorescens HK44 was monitored noninvasively in quartz sand under unsaturated-flow conditions within a 45- by 56- by 1-cm two-dimensional light transmission chamber. The spatial and temporal development of growth were mapped daily over 7 days by quantifying salicylate-induced bioluminescence. A nonlinear model relating the rate of increase in light emission after salicylate exposure to microbial density successfully predicted growth over 4 orders of magnitude (r(2) = 0.95). Total model-predicted growth agreed with growth calculated from the mass balance of the system by using previously established growth parameters of HK44 (predicted, 1.2 x 10(12) cells; calculated, 1.7 x 10(12) cells). Colonization expanded in all directions from the inoculation region, including upward migration against the liquid flow. Both the daily rate of expansion of the colonized zone and the population density of the first day's growth in each newly colonized region remained relatively constant throughout the experiment. Nonetheless, substantial growth continued to occur on subsequent days in the older regions of the colonized zone. The proportion of daily potential growth that remained within the chamber declined progressively between days 2 and 7 (from 97 to 13%). A densely populated, anoxic region developed in the interior of the colonized zone even though the sand was unsaturated and fresh growth medium continued to flow through the colonized zone. These data illustrate the potential of a light transmission chamber, bioluminescent bacteria, and sensitive digital camera technology to noninvasively study real-time hydrology-microbiology interactions associated with unsaturated flow in porous media.

A model that uses the induction phase of lux gene-dependent bioluminescence in Pseudomonas fluorescens HK44 to quantify cell density in translucent porous media.

A cooled charge-coupled device (CCD) camera was used to follow the kinetics of induction of lux gene-dependent bioluminescence in Pseudomonas fluorescens HK44 held either in aqueous suspensions minus sand, saturated or unsaturated translucent sand (0.348 and 0.07 cm(3) H(2)O/cm(3) of sand, respectively), and at cell densities ranging between 1 x 10(6) and 8.5 x 10(8) cells/ml. Before O(2) availability became a limiting factor, the rate of light emission (L) increased with the square of time (t) and linearly with increasing cell density (c). A nonlinear model was developed that contains a "rate of increase in light emission" constant, B', which is determined directly from the slope of a plot of radical L/c against t. The model predicted the behavior of lux induction in HK44 under a variety of conditions. Similar B' values were determined [49.0-57.6 x 10(-10) light units/(cell min(2))] for cell suspensions held in aqueous medium minus sand, in saturated or unsaturated 40/50 grade sand (0.36 mm grain diameter) and in two other textural classes of translucent sand. Although both the growth phase, and the presence of glucose during lux induction affected the first detectable time (FDT) of bioluminescence by HK44 in sand, the kinetics of induction of light emission were similar among treatments (stationary phase cells plus glucose, B'=61.6+/-3.2, log phase cells plus glucose, B'=63.2+/-7.2). The potential exists to use a combination of a CCD camera system, an inducible lux gene containing bioluminescent bacterium, and a light transmission chamber to nonintrusively visualize and quantify in real time the interactions between bacterial growth and unsaturated flow of water and solutes in porous media.

A modification to the Bouwer and Rice method of slug-test analysis for large-diameter, hand-dug wells.

The Bouwer and Rice method of estimating the saturated hydraulic conductivity (Ks) from slug-test data was evaluated for geometries typical of hand-dug wells. A two-dimensional, radially symmetric and variably saturated, ground water transport model was used to simulate well recovery given a range of well and aquifer geometries and unsaturated soil properties, the latter in terms of the van Genuchten parameters. The standard Bouwer and Rice method, when applied to the modeled recharge rates, underestimated Ks by factors ranging from 1.3 to 5.6, depending on the well geometry and the soil type. The Bouwer and Rice analytical solution was modified to better explain the recovery rates as predicted by the numerical model, which revealed a significant dependence on the unsaturated soil for the shallow and wide geometries that are typical of traditional wells. The modification introduces a new parameter to the Bouwer and Rice analysis that is a measure of soil capillarity which improves the accuracy of Ks estimates by tenfold for the geometries tested.

Numerical estimation of multicomponent adsorption isotherms in preparative chromatography: implications of experimental error.

Since experimental methods for measuring multicomponent adsorption isotherms are extremely tedious, numerical approaches are an attractive alternative. Here, the variance in isotherm parameters as a function of experimental error in measured effluent concentrations is quantified. The number of experimental replicates needed to obtain isotherm parameters to a desired level of accuracy is calculated explicitly. After the covariance matrix of the parameters has been determined, Monte Carlo methods are found to be rapid and effective. The use of different kinds of experiments, the effect of resolution and loading, and the impact of the number of measured data points are described.

Mitochondrial DNA depletion causes morphological changes in the mitochondrial reticulum of cultured human cells.

Depletion of mitochondrial DNA (mtDNA) causes defects in respiratory activity and energy production. Recent studies have shown mitochondria to exist primarily as reticular networks, having tubular cristae. Using fluorescence microscopy and transmission electron microscopy, we have examined mitochondrial morphology and interior structure in wildtype and mtDNA-depleted rho0 human fibroblasts and 143B osteosarcoma cell lines. MtDNA depletion results in compromise of the mitochondrial continuum and causes a reduction in amount of cristal membranes, often prompting the remaining cristae to adopt a circular appearance in the mitochondrial interior. These changes emphasize the tight relationship between mitochondrial structure and function.

Biophysical mechanisms for morphogenetic progressions at the shoot apex.

Leaf primordia, first visible as small bumps, are produced in a cyclical pattern at the edges of the shoot apex, a smooth region at the top of the stem. Their formation is a biomechanical process. This review first considers hypothetical construction mechanisms and then summarizes research that provides information about how and where the primordia are made. Studies of growth at the primordium site indicate the importance of growth parallel to the surface in generating the forces for primordium emergence. The symmetry of the pattern of reinforcement by cellulose microfibrils correlates with the subsequent pattern of primordium production. Finite element models of the apex reveal that lateral bulging of the apex results in a gradient of shear stress, with high shear at the future primordium site. In contrast, tension parallel to the surface is lowest at the primordium site. Response of apical surface tissue to punctures indicates that an existing primordium can exert a pulling force tangential to its base and a compressive force perpendicular to its base. These observations lead to identification of a continuous biophysical cycle for apex morphogenesis, in which most of the steps are direct physical consequences of the previous step. Biophysical processes, subject to input from genetic, hormonal, and environmental sources, are thus involved in the construction and patterning of leaf primordia.

Spatial relationships between uninfected and infected cells in root nodules of soybean.

In soybean (Glycine max (L.) Merr.) the uninfected cells of the root nodule are responsible for the final steps in ureide production from recently fixed nitrogen. Stereological methods and an original quantitative method were used to investigate the organization of these cells and their spatial relationships to infected cells in the central region of nodules of soybean inoculated with Rhizobium japonicum strain USDA 3I1B110 and grown with and without nitrogen (as nitrate) in the nutrient medium. The volume occupied by the uninfected tissue was 21% of the total volume of the central infected region for nodules of plants grown without nitrate, and 31% for nodules of plants grown with nitrate. Despite their low relative volume, the uninfected cells outnumbered the much larger infected cells in nodules of plants grown both without and with nitrate. The surface density of the interface between the ininfected and infected tissue in the infected region was similar for nodules in both cases also, the total range being from 24 to 26 mm(2)/mm(3). In nodules of plants grown without nitrate, all sampled infected cells were found to be in contact with at least one uninfected cell. The study demonstrates that although the uninfected tissue in soybean nodules occupies a relatively small volume, it is organized so as to produce a large surface area for interaction with the infected tissue.

Organogenesis in Graptopetalum paraguayense E. Walther: shifts in orientation of cortical microtubule arrays are associated with periclinal divisions.

The interior of a new lateral organ, such as a leaf, arises from the products of periclinal divisions of sub-epidermal cells. The biophysical basis of the elongation of such a new axis is transverse (hoop) reinforcement of the cells by cellulose in the primary walls. This structural polarity is associated with transverse alignment of cortical microtubules. We have brought the histological and biophysical views together by showing that the new, periclinal, divisions are a prerequisite for a corresponding change in the orientation of the microtubular array in the daughter cells. Investigation of this relationship required development of criteria for assessing the predominant orientation of a microtubule array in a single section of known orientation. By obtaining information about the predominant orientation of microtubule arrays in the sub-epidermal cells, we were able to study structural polarity shifts which occurred as a detached leaf of Graptopetalum produced a new shoot. During organogenesis, the new polarity is seen only in cells which have divided periclinally. Following single periclinal divisions, cells are seen with microtubules in the old or new orientation or in a mixture of different orientations. Cells with more than one orientation of microtubules are probably at intermediate stages in the shift to the new polarity. Among cells which have undergone two consecutive periclinal divisions, the old polarity is no longer seen, all cells having high frequencies of microtubules in the new orientation. Such cells are either polarized in the new direction or nonpolarized. The shifts in polarity of the cells in the interior anticipate the appearance of the first leaf primordia. However, contrary to the expectations from the histological view of organogenesis, these shifts do not dominate the process. Concurrent polarity changes in the epidermis appear at least as important.