Patterns of mitochondrial DNA instability in Brassica campestris cultured cells

We previously showed that the mitochondrial DNA (mtDNA) of a Brassica campestris callus culture had undergone extensive rearrangements (i.e. large inversions and a duplication) relative to DNA of the control plant [54]. In this study we observed that after continued growth, the mtDNA of this culture continues to change, with rearranged forms amplifying and diminishing to varying proportions. Strikingly similar changes were detected in the mtDNA profiles of a variety of other long- and short-term callus and cell suspension lines. However, the proportions of parental (‘unrearranged’) and novel (‘rearranged’) forms varied in different cultured cell mtDNAs. To address the source of this heterogeneity, we compared the mtDNA organization of 28 individual plants from the parental seed stock. With the exception of one plant containing high levels of a novel plasmid-like mtDNA molecule, no significant variation was detected among individual plants and therefore source plant variation is unlikely to have contributed to the diversity of mitochondrial genomes observed in cultured cells. The source of this culture-induced heterogeneity was also investigated in 16 clones derived from single protoplasts. A mixed population of unrearranged and rearranged mtDNA molecules was apprent in each protoclone, suggesting that the observed heterogeneity in various cultures might reflect the genomic composition of each individual cell; however, the induction of an intercellular heterogeneity subsequent to the protoplast isolation was not tested and therefore cannot be ruled out. The results of this study support our earlier model that the rapid structural alteration of B. campestris mtDNA in vitro results from preferential amplification and reassortment of minor pre-existing forms of the genome rather than de novo rearrangement. Infrequent recombination between short dispersed repeated elements is proposed as the underlying mechanism for the formation of these minor mtDNA molecules.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43428/1/11103_2004_Article_BF00017914.pd

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

SLIDES: Groundwater-Surface Water Interactions

Presenter: Thomas Maddock III, Department of Hydrology, University of Arizona. 16 slides

A riparian evapotranspiration package for MODFLOW-2000 and MODFLOW-2005

A new version of an evapotranspiration package for the U.S. Geological Survey's groundwater -flow model, MODFLOW, is documented. The Riparian Evapotranspiration Package (RIP-ET) provides flexibility in simulating riparian and wetland evapotranspiration (ET) not provided by the MODFLOW -2000 and MODFLOW 2005 traditional Evapotranspiration (EVT) Package, nor by the MODFLOW-2000 Segmented Function Evapotranspiration (ETS1) Package. This report describes how the package was conceptualized and provides input instructions, listings and explanations of the source code, and an example simulation. Traditional approaches to modeling ET processes assume a piecewise linear relationship between ET flux rate and hydraulic head. The RIP-ET replaces this traditional relationship with a segmented, nonlinear dimensionless curve that reflects the eco-physiology of riparian and wetland ecosystems. Evapotranspiration losses from these ecosystems are dependent not only on hydraulic head but on the plant types present. User -defined plant functional groups (PFGs) are used to elucidate the interactive processes of plant ET with groundwater conditions. Five generalized plant functional groups based on transpiration rates, plant rooting depth, and water tolerance ranges are presented: obligate wetland, shallow-rooted riparian, deep- rooted riparian, transitional riparian and bare ground /open water. Plant functional groups can be further divided into subgroups (PFSG) based on plant size, density or other user defined field. The RIP -ET allows for partial habitat coverage and mixtures of plant functional subgroups to be present in a single model cell. Habitat areas are designated by polygons. A polygon can contain a mixture of PFSGs and bare ground, and is assigned a calculated land surface elevation. This process requires a determination of fractional coverage for each of the plant functional subgroups present in a polygon to simulate the mixture of coverage types and resulting ET. The fractional cover within a cell has two components: 1) the polygonal fraction of active habitat in a cell, and 2) fraction of plant flux area in a polygon. The RIP -ET determines the ET rate for each plant functional group in a cell, the total ET in the cell, and the total ET rate over the region of simulation.This research was supported in part by two grants. The first was an EPA -NSF Star Grant entitled "Restoring and Maintaining Riparian Integrity in Arid Watersheds," number R827150/01, which funded field experiments in the South Fork of the Kern River in California and the San Pedro River in Arizona. The second was an NCEA Global Change Division CO -OP Agreement entitled "Potential Effects of Climate Change on Biodiversity and Riparian Wildlife Habitat of the Upper San Pedro River," which funded development of this software package. The views and conclusions contained in this document are those of the authors and should not necessarily be interpreted as representing official policies, (expressed or implied) of the EPA or NCEA. We would like to thank our fellow grantees Julie Stromberg, Robert Glennon, and Bonnie Colby, who worked with us on the EPA -NSF project, and Jeff Price and again Julie Stromberg, who, worked with us on the NCEA project. A thank you also to our colleagues Bob MacNish, Phil Guertin, David Goodrich, Jim Shuttleworth, Paul Brooks and Ty Ferre. Thanks to the students that worked at the Kern River site: Asia Philben, Tom D. Maddock, Phil Bredfelt, Clair Tomkins and Chris Adams; and the students who worked at the tree torture site along the San Pedro River: Marla Odum, Kathleen McHugh, Asia Philben, Gerd Von Glinski, and Tom D. Maddock. We gratefully acknowledge the Palominas Trading Post without whose support the San Pedro project could not have been completed. Thanks also to Reed Tollifson and Jeff King at the Audubon Kern River Preserve, and a special thank you to Carolyn Dragoo for her assistance and support. This second version of RIP -ET has evolved from experiences in application to MODFLOW models of the South Fork Kern River Valley, California; the Lower Rio Grande Basin, New Mexico; Arivaca Watershed, Arizona; the Upper San Pedro River Basin, Arizona; and the Colorado River Delta, Mexico. We have also had written and verbal communications from a variety of users throughout the United States and a broad. Coding help has come from Arlen Harbough, Stan Leakes and Randy Hanson of the U.S. Geological Survey. In this go around, special thanks are in order for Hoori Ajami.This title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]

Flow model for the Bingham cienega area, San Pedro river basin, Arizona: a management and restoration tool

A finite element groundwater flow model was used to support a hydrologic assessment for a study area in the Lower San Pedro River Basin which contains the Bingham Cienega. Consolidated sedimentary rocks associated with an extension of the Catalina Core Complex truncate the floodplain aquifer system in the study area. The elevated water table produced by this "hardrock" results in spring discharge at the cienega and a locally gaining reach of the San Pedro River. The steady -state model suggests that recharge (and discharge) components for the floodplain aquifer sum to 3.10 cfs. Mountain front recharge, underflow, and stream leakage are the primary recharge mechanisms, while stream leakage, evapotranspiration, spring flow, and underflow out are sources for groundwater discharge. A steady -oscillatory model was used to account for seasonal periodicity in the system's boundary conditions. Monthly variation in the evapotranspiration rate was offset primarily by storage changes in the aquifer. Due to a lack of measured hydrologic data within the study area, results from the model simulations are only preliminary. Model development and the subsequent sensitivity analyses have provided insight into what type of data needs to be collected. Head measurements are most needed in the area just downstream from Bingham Cienega. The mountain front recharge and evapotranspiration rates are shown to be highly sensitive parameters in the model; improved estimation of these values would be helpful. Spring discharge would be a valuable calibration tool if it could be accurately measured. A more extensive record of stream baseflow in the San Pedro River should be established. After more hydrologic data is collected, the model could be recalibrated so as to better represent the system. Eventually, this tool may be used in direct support of management and/or restoration decisions.Research and development for this project was funded in part by the Arizona Chapter of The Nature Conservancy. The views and conclusions reported are those of the author and are not necessarily shared by The Nature Conservancy. We would like to give special thanks to Robert Mac Nish, Kate Baird and Kevin Lansey for their thoughtful comments on this document.This title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]

Modeling of Ground-Water Flow and Surface/Ground-Water Interaction for the San Pedro River Basin Part I Mexican Border to Fairbank, Arizona

Many hydrologic basins in the southwest have seen their perennial streamflows turn to ephemeral, their riparian communities disappear or be jeopardized, and their aquifers suffer from severe overdrafts. Under -management of ground -water exploitation and of conjunctive use of surface and ground waters are the main reasons for these events.Research and development was supported in part by the Cochise County Flood Control District, under grant provided by them. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the Cochise County Flood Control District. We would like to thank the members of the Upper San Pedro Water Management Council (USPWMC) for there timely input and advice. This group contributed a positive aspect to this endeavor. Special thanks to Eric Korsten and Ben Lomeli whose sometime opposing views kept the authors on their tippy -tippy toes, to Dennis Sundie whose love of cloud seeding is only surpassed by his patience in guiding the USPWMC, to Bob McNish for acting as our guru and to Don Henderson for trying to keep us technocrats focused on the real world.This title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]

Simulation of Groundwater Conditions in the Upper San Pedro Basin for the Evaluation of Alternative Futures

The creation of the groundwater model of the Upper San Pedro Basin included two developmental phases: the creation of a conceptual and numerical model. The creation of the conceptual model was accomplished through the utilization of Geographic Information System (GIS) software, namely ArcView, used primarily to view and create point, line, and polygonal shapes. The creation of a numerical model was accomplished by the infusion of the conceptual model into a 3D finite difference grid used in MODFLOW groundwater software from the U.S. Geological Survey. MODFLOW computes the hydraulic head (water level) for each cell within the grid. The infusion of the two models (conceptual and numerical) was allowed through the use of Department of Defense Groundwater Modeling System (GMS) software. The time period for groundwater modeling began with predevelopment conditions, or "steady state." Steady state conditions were assumed to exist in 1940. The steady state was used as the initial condition for the subsequent transient analysis. The transient simulation applied historical and current information of pumping stresses to the system from 1940 to 1997. After modeling current conditions, Alternative Futures' scenarios were simulated by modifying current stresses and by adding new ones. The possible future impacts of to the hydrologic system were then evaluated.This title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]

MODRSP: a program to calculate drawdown, velocity, storage and capture response functions for multi-aquifer systems

MODRSP is program used for calculating drawdown, velocity, storage losses and capture response functions for multi - aquifer ground -water flow systems. Capture is defined as the sum of the increase in aquifer recharge and decrease in aquifer discharge as a result of an applied stress from pumping [Bredehoeft et al., 19821. The capture phenomena treated by MODRSP are stream- aquifer leakance, reduction of evapotranspiration losses, leakance from adjacent aquifers, flows to and from prescribed head boundaries and increases or decreases in natural recharge or discharge from head dependent boundaries. The response functions are independent of the magnitude of the stresses and are dependent on the type of partial differential equation, the boundary and initial conditions and the parameters thereof, and the spatial and temporal location of stresses. The aquifers modeled may have irregular -shaped areal boundaries and non -homogeneous transmissive and storage qualities. For regional aquifers, the stresses are generally pumpages from wells. The utility of response functions arises from their capacity to be embedded in management models. The management models consist of a mathematical expression of a criterion to measure preference, and sets of constraints which act to limit the preferred actions. The response functions are incorporated into constraints that couple the hydrologic system with the management system (Maddock, 1972). MODRSP is a modification of MODFLOW (McDonald and Harbaugh, 1984,1988). MODRSP uses many of the data input structures of MODFLOW, but there are major differences between the two programs. The differences are discussed in Chapters 4 and 5. An abbreviated theoretical development is presented in Chapter 2, a more complete theoretical development may be found in Maddock and Lacher (1991). The finite difference technique discussion presented in Chapter 3 is a synopsis of that covered more completely in McDonald and Harbaugh (1988). Subprogram organization is presented in Chapter 4 with the data requirements explained in Chapter 5. Chapter 6 contains three example applications of MODRSP.Research and development was supported in part by the U.S. Geological Survey, Department of the Interior, under USGS award number 14-08- 0001- G1742. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U. S. Government.This title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]

MR2K: A program to calculate drawdown, velocity, storage and capture response functions

A program, MR2K, used for calculating drawdown, velocity, storage loss, and capture response functions for multi -aquifer groundwater flow systems was developed. Capture is defined as the sum of the increase in aquifer recharge and decrease in aquifer discharge as a result of an applied stress from groundwater pumping. The capture phenomena treated are stream-aquifer leakance, reduction of evapotranspiration losses, reduction of drain flows, flows to and from prescribed head boundaries, and increases or decreases in natural recharge or discharge from head-dependent boundaries. The response functions are independent of the magnitude of the pumping stresses, and are dependent on the type of partial differential equation, boundary and initial conditions and the parameters thereof, and the spatial and temporal locations of stresses. The aquifers modeled may have irregular- shaped boundaries and nonhomogeneous transmissive and storage qualities. The stresses are groundwater withdrawals from wells. The utility of response functions arises from their capacity to be embedded in management models such as decision support systems. The response functions are incorporated into the objective function or constraints that couple the hydrologic system with the management system. Three response -function examples are presented for a hypothetic basin.Research and development for MR2K was supported in part by the National Science Foundation Science and Technology Center for Sustainabliity of Semi-Arid Hydrology and Riparian Areas (SAHRA). The original MODRSP software was supported in part by the U.S. Geological Survey under award number 14-08-0001-G1742. The view and conclusions contained in this document are those of the authors and should not be interpted as necessarily representing the official policies, either expressed or implied of the U.S. Government.This title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]

STREAM-AQUIFER INTERACTION MODELING IN LOWER CIENEGA CREEK BASIN, ARIZONA USING FINITE ELEMENTS

Only a few areas in the deserts of the southwestern United States possess perennial streamflows. Cienega Creek near Tucson, Arizona is one of them (Figurel). Because of ground -water punping, some of these streams are in jeopardy of becoming ephemeral. The variability of surface water supply in the southwestern United States is very important because of its effects on riparian systems. Declines in water table and ground -water storage (over - exploitation of pumping wells) pose major concern as land subsidence and earth fissures, and produce stream and vegetation losses through ground and surface -water interactions. This report examines the Lower Cienega Creek Basin (LCCB) and the potential impact of nearby commercial development on the perennial stream. This area was chosen because it contains a natural preserve and a perennial stream. Perennial water flow and shallow water levels along the creek support various riparian species which shelter many types of insects and wildlife. The stream contained several species of fish including the endangered Gila Topminnow before they were extinct from this creek. This natural preserve, near the basin's exit, is one of the few desert places in the U.S. supporting a suitable habitat for animals, birds, and fishes because of its lush vegetation. An important riparian indicator for water table levels are cottonwood trees. These trees require shallow water to survive. As water levels decline, the cottonwoods produce less leaves. These cottonwoods could limit their existence by ceasing reproduction. Ultimately, a detrimental impact will be noticed in the surrounding ecosystem.During the Fall semester 1993, the Department of Hydrology and Water Resources initiated a thesis practicum allowing students to complete a Master's thesis within a year by participating in a group project. The project is divided topically, with each student in charge of a specific topic, resulting in a thesis and a HWR Series report. The group project covers each of the departmental focal areas: surface -water hydrology, subsurface hydrology, water chemistry, and water resources administration. This report is based on a thesis from the Fall 1993 - Spring 1994 project focusing on the water resources of the Lower Cienega Creek Basin, Arizona. This basin encompasses Pima Count's Cienega Creek Natural Preserve, located about 25 miles southeast of Tucson. The basin includes perennial stream reaches at the "Narrows" and within the preserve. These flows support a lush riparian population, one of the few remaining in the state. The goals of this project were tp provide insight into hydrological processes with in the basin and to recommend management alternatives. The following are faculty participants: Nathan Bums Leo Leonhart Martha Conklin Tom Maddock III Don Davis L. G. Wilson Simon InceThis title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]