[1998]. They designed a compartmental liquid sampler, which was inserted into a horizontal borehole, to collect infiltrating solution at multiple locations. They estimated the amount of water flowing through the fractures and imbibing into the matrix across the fracture walls and determined that under variable moisture content conditions the fracture aperture, roughness, and flow channels varied with time. They also noted that under field conditions the effective fracture aperture was more than 1 order of magnitude smaller than that expected based on laboratory conditions. Or and Ghezzehei [2000] studied water dripping into subterranean cavities in a fractured porous medium in order to improve estimates of dripping rates onto waste disposal canisters placed in caverns. These results suggest that conventional approaches and concepts, such as Darcy flow through a constant fracture aperture, may not be valid for characterizing unsaturated fractured rocks.Several laboratory-scale investigations were conducted using natural fracture cores and fracture replicas to investigate factors and processes affecting flow and transport under con- In 1996, three groups of 16 wells were drilled to install monitoring instrumentation, including vertical wells of series T (depths of 3-6.7 m), and inclined wells (270-45 ø from vertical) of series E and R (lengths of 18.3-22.9 m). In 1997, after interpretation of the results of the 1996 infiltration test, which showed a zone of preferential flow between wells R1 and R2, two additional inclined wells (R5 and R6) were drilled between existing R wells. Note that inclined boreholes were mostly drilled from the outside of the pond to reduce the disturbance to the pond surface and to intersect more vertical columnbounding fractures to better characterize the three-dimensional geometry of flow below the pond.The types of instrumentation used during the infiltration tests are summarized in Table 1. A more detailed description of the instrumentation is given by Faybishenko et al. [1998b]. All the instruments were installed in boreholes using the following method of borehole completion [Faybishenko et al., 1998d]. The instruments were attached to the outer faces of polyethylene packers mounted onto sections of 3.5-crn OD PVC manchette pipe, and the sections were glued together to form a continuous string of instruments placed at preselected depths. After the string with the probes was lowered into a borehole, the packers and the space between the packers were infilled with impermeable polyurethane resin, thus pressing the instruments against the borehole walls. This completion method ensured that no water flow occurred through the bore- small trench (15 cm high by 15 cm wide) was cut into the basalt at the location of the previous berm and a permanent concrete wall was constructed that practically eliminated water leakage beneath and through the berm. The experimental data and fitting curves are shown in Figure 6, and the fitting parameters for each test, which were determined using a lea...

Background: Iron homeostasis of Shewanella oneidensis, a γ-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis.

A conceptual model of the geometry and physics of water flow in a fractured basalt vadose zone was developed based on the results of lithological studies and a series of ponded infiltration tests conducted at the Box Canyon site near the Idaho National Engineering and Environmental Laboratory (INEEL) in Idaho. The infiltration tests included one two-week test in 1996, three two-day tests in 1997, and one four-day test in 1997. For the various tests, initial infiltration rates ranged from 4.1 cm/day to 17.7 cm/day and then decreased with time, presumably due to mechanical or microbiological clogging of fractures and vesicular basalt in the near-surface zone, as well as the effect of entrapped air. The subsurface moisture redistribution was monitored with tensiometers, neutron logging, time domain reflectrometry and ground penetrating radar. A conservative tracer, potassium bromide, was added to the pond water at a concentration of 3 gIL to monitor water flow with electrical resistivity probes and water sampling. Analysis of the data showed evidence of preferential flow rather than the propagation of a uniform wetting front. We propose a conceptual model describing the saturationdesaturation behavior of the basalt, in which rapid preferential flow through vertical column-bounding fractures occurs from the surface to the base of the basalt flow. After the rapid wetting of column-bounding fractures, a gradual wetting of other fractures and the basalt matrix occurs. Fractures that are saturated early in the tests may become desaturated thereafter, which we attribute to the redistribution of water between fractures and matrix. Lateral movement of water was also observed within a horizontal central fracture zone and rubble zone, which could have important implications for contaminant accumulation at contaminated sites.

1Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter 2 plates is an emerging technology that allows a high throughput survey of the growth and 3 physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a swift 4 method for phenotypic analysis is invaluable, not only to serve as a starting point for further 5 evaluation, but also to provide a broad understanding of the physiology of an uncharacterized 6 wild-type organism or the physiology/phenotype of a newly created mutant of that organism. 7Given recent advances in genetic characterization and targeted mutations to elucidate genetic 8 networks and metabolic pathways, high-throughput methods for determining phenotypic 9 differences are essential. Here we outline challenges presented in studying the physiology 10 and phenotype of a sulfate-reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris 11Hildenborough. Modifications of the commercially available OmniLog TM system (Hayward, 12 CA) for experimental setup, and configuration, as well as considerations in PM data analysis 13 are presented. Also highlighted here is data viewing software that enables users to view and 14 compare multiple PM data sets. The PM method promises to be a valuable strategy in our 15 systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic 16 and aerobic bacteria. 17 18 Introduction 1Desulfovibrio vulgaris Hildenborough, a sulfate-reducing anaerobic, delta 2 proteobacterium, has been identified as a model organism in many types of sulfate-reducing 3 environments, especially those related to metal-contaminated sites (Caumette 1993; Telang, 4 Voordouw et al. 1994;Noguera, Brusseau et al. 1998;Cottrell and Cary 1999; Wind, Stubner 5 et al. 1999; Heidelberg, Seshadri et al. 2004). Detailed studies on growth and metabolism of 6 this organism are necessary to understand metal reduction processes under a variety of 7 environmental conditions. Conducting a growth curve to determine lag time, growth rate, and 8 maximum cell densities often is necessary to understand the physiology or phenotype and the 9 specific effect of environmental stressors on the organism. Culturing in batch cultures has the 10 disadvantage of large amounts of media with single or multiple component differences, of 11 large numbers of tubes or flasks, and of the inconvenience of manually monitoring optical 12 densities of large numbers of cultures. In addition, growth times often are difficult to predict 13 and key experimental data may be lost if sampling is not sufficiently frequent (Sani, Peyton et 14 al. 2003). Increased convenience and quantity of the data can be obtained by automation of 15 the growth curve measurements in 96-well microtiter plates (hereafter referred to as plates). 16After preparation, plates can be incubated and growth monitored by recording opacity changes 17 by automation at discrete intervals, continuously over several days. Microtiter plate readers can rapidly measure tur...

The stage-discharge curve for a complex spillway geometry has been computed with a three-dimensional numerical model. The model solved the Reynoldsaveraged Navier-Stokes equations using the k-å turbulence model. An orthogonal fixed grid was used, where the cells could be wet, dry or partially wet. A volume-of-fluid method was used to compute the location of the free surface in the grid. The spillway consisted of four partly separated free overflow chambers, with tunnel outlets. The four tunnels joined in a collection tunnel where free surface occurred in some sections and filled the tunnel in others. The resulting stage-discharge curve, therefore, showed two parts: one for low discharges with dominantly free surface flow in the tunnels and another part when the tunnels were filled. The results were compared with a physical model study. The deviation between the computed and measured values of the rating curve were under 2% for most of the curve, but rose to a maximum value of 10% where the flow was most complex. The findings indicate that a three-dimensional numerical model can be an accurate, inexpensive and rapid tool to predict the stage-discharge curve for complex spillways.