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Optimal In-Situ Bioremediation System Design Using Parallel Recombinative Simulated Annealing, Horng-Jer Shieh, Richard C. Peralta

Civil and Environmental Engineering Faculty Publications

Presented is a simulation/optimization (S/0) model combining optimization with BIOPLUME II simulation for optimizing in-situ bioremediation system design. The (S/0) model uses parallel recombinative simulated annealing to search for an optimal design and applies the BIOPLUME II model to simulate aquifer hydraulics and bioremediation. Parallel recombinative simulated annealing is a general-purpose optimization approach that has the good convergence of simulated annealing and the efficient parallelization of a genetic algorithm. We propose a two-stage management approach. The first stage design goal is to minimize total system cost (pumping/treatment, well installation and facility capital costs). The second stage design goal is to …

A Landowner's Guide To Common North American Predators Of Upland Nesting Birds, T. A. Messmer, Michael R. Conover, Raymond Dueser, P. W. Klimack

Wildland Resources Faculty Publications

This publication provides information designed to increase the reader’s basic understanding of predator/prey interactions and the biology and ecology of common North American predators of upland-nesting birds, their nests, and young. We also discuss the potential impacts of these predators on upland-nesting bird populations. By understanding the biology and ecology of predators, the reader will be better prepared to make informed management decisions about how to enhance local upland-nesting bird populations. Information regarding specific techniques that can be used to manage common predators of upland-nesting birds, can be found in an accompanying publication entitled, “A Landowner’s Guide to Managing …

Alternative Futures For The Region Of Camp Pendleton California U.S.A. Oak Grove Valley, Richard E. Toth

Environment and Society Faculty Publications

The U.5. Environmental Protection Agency's (EPA Science Advisory Board, in its report Reducing Risk: Priorities and Strategies for Environmental Protection (U.S. EPA, 1990), identified the highest priority environmental risks to the United States, based primarily on geographic extent and irreversibility of effects. Habitat modification and loss of species diversity were ranked at the highest level of ecological risk. Habitat and species diversity are tightly coupled; species diversity at a regional level cannot be maintained without maintaining quality habitat. The Science Advisory Board expressed the view shared by many ecologists that natural habitats and their associated assemblages of plants and animals …

Managing Problems Caused By Urban Canada Geese, A. L. Gosser, Michael R. Conover, Terry A. Messmer

Wildland Resources Faculty Publications

Canada geese (Branta canadensis) started nesting in urban areas during the past 50 years. Today, most urban areas in the U. S. and Canada support breeding populations of these birds. Many of these resident goose populations are the result of a successful effort by fish and wildlife agencies to restore populations of giant Canada goose (Branta canadensis maxima), which is the largest of the 11 races of Canada geese. Their large body mass enables them to survive colder temperatures; thus, they tend to winter as far north as open water can be found.

Landscape Cover-Type Modeling Using A Multi-Scale Thematic Mapper Mosaic, Collin G. Homer, R. Douglas Ramsey, Thomas C. Edwards Jr., Allan Falconer

Wildland Resources Faculty Publications

Landscape ecological applications of remotely sensed data are needed over increasingly larger areas and at finer spatial scales. Within the framework of the National Biological Service Gap Analysis program, 36 Utah cover types were modeled from a state-wide Landsat TM mosaic created from 24 scenes at 30-metre resolution (219,883 sq km). The state was subset into three ecoregions for classification, with cover-type association to spectral classes defined using a two-step modeling approach. Steps included post-classification correlation of 1,758 state-wide field training sites to spectral classes, and post-classification ancillary GIS modeling using ecological parameters of elevation, slope, aspect, and location to …

Growth And Survival Of Colorado Squawfish In The Upper Colorado River, D. B. Osmundson, Ronald J. Ryel, T. E. Mourning

Wildland Resources Faculty Publications

Growth and adult survival rates were estimated for the endangered Colorado squawfish Ptychocheilus lucius inhabiting the upper Colorado River by using data from fish captured during 1990–1995. Mean annual growth rates of fish aged 3–6 years ranged from 32.2 (age 6) to 82.0 (age 3) mm/year. Growth rates for older fish were highest for fish 400–449 mm total length, TL, (42.7 mm/year) and declined to 19.8 mm/year for fish 500–549 mm TL. Fish 550 mm and longer grew an average 9.5 mm/year. Survival rates for fish 550 mm and longer were estimated by comparing measured size distributions with simulated stable …

Correlated Confocal And Intermediate Voltage Electron Microscopy Imaging Of The Same Cells Using Sequential Fluorescence Labeling, Fixation, And Critical Point Dehydration, Lee D. Peachey, Harunori Ishikawa, Tohru Murakami

Scanning Microscopy

Confocal laser scanning microscopy (CLSM) and intermediate voltage transmission electron microscopy (IVEM) each has its own particular advantages. CLSM can examine living cells, but is particularly useful when applied to cells that have been lightly fixed, permeabilized, and stained with fluorescent-labeled antibodies for localization of specific molecular species at the resolution of the light microscope while still in the hydrated state. IVEM provides much higher resolution images, but requires more drastic preparation procedures, including dehydration. This paper presents methods for combining these complementary approaches to examine exactly the same cells sequentially by CLSM and IVEM. Cells are grown in culture …

Immunocytochemistry By Electron Spectroscopic Imaging Using Well Defined Boronated Monovalent Antibody Fragments, M. M. Kessels, B. Qualmann, W. D. Sierralta

Scanning Microscopy

Contributing to the rapidly developing field of immunoelectron microscopy a new kind of markers has been created. The element boron, incorporated as very stable carborane clusters into different kinds of peptides, served as a marker detectable by electron spectroscopic imaging (ESI) - an electron microscopic technique with high-resolution potential.

Covalently linked immunoreagents conspicuous by the small size of both antigen recognizing part and marker moiety are accessible by using peptide concepts for label construction and their conjugation with Fab' fragments. Due to a specific labeling of the free thiol groups of the Fab' fragments, the antigen binding capacity was not …

In Situ Hybridization, In Situ Transcription, And In Situ Polymerase Chain Reaction, L. E. De Bault, J. Gu

Scanning Microscopy

In situ hybridization, in situ transcription, and in situ polymerase chain reaction (PCR) are techniques used to detect DNA and RNA sequences within a cell or tissue structure. These three in situ methodologies employ the principles of recombinant DNA to form double-stranded hybrids of DNA-DNA, DNA-RNA, or RNA-RNA. The essence of in situ hybridization (ISH) is the hybridization of a labeled probe to a complementary target sequence, whereas in situ transcription (IST) is the synthesis of complementary DNA incorporating a label directly on the target DNA or RNA within a cell or tissue. In the case of in situ PCR …

Microscopic Analysis Of Dna And Dna-Protein Assembly By Transmission Electron Microscopy, Scanning Tunneling Microscopy And Scanning Force Microscopy, T. Müller-Reichhert, H. Gross

Scanning Microscopy

To investigate DNA and DNA-protein assembly, nucleic acids were adsorbed to freshly cleaved mica in the presence of magnesium ions. The efficiency of DNA adhesion and the distribution of the molecules on the mica surface were checked by transmission electron microscopy. In addition, various kinds of DNA-protein interactions including DNA wrapping and DNA super-coiling were analyzed using electron microscopy. In parallel, this Mg²⁺/mica method can be applied (1) to analyze embedded DNA by scanning tunneling microscopy, (2) to visualize freeze-dried, metal coated DNA-protein complexes by tunneling microscopy, and (3) to image DNA or DNA-protein interaction in air or …

Preparation Of Samples For Polymerase Chain Reaction In Situ, Gerard J. Nuovo

Scanning Microscopy

The purpose of this paper is to describe the key variables in sample and reagent preparation needed for successful polymerase chain reaction (PCR) in situ. Tissue or cell preparations should be fixed in a cross linking fixative, such as 10% buffered formalin, preferably from 15 to 48 hours. Tissues should be embedded in paraffin; cell preparations can be fixed when near confluence, then physically removed and processed. When possible three samples (4 μM tissue sections or 1-5000 cells) should be placed on silane coated glass slides. Digestion in pepsin (2 mg/ml) for 30 min is adequate for DNA detection …

Aspects Of Cryofixation And Cryosectioning For The Observation Of Bulk Biological Samples In The Hydrated State By Cryoelectron Microscopy, K. Richter

Scanning Microscopy

Cryoelectron microscopy allows the observation of hydrated samples at high spatial resolution, and it would be of great interest in biology to apply this method to cells and tissues. However, because of technical problems, the cryo-observation of frozen hydrated ultrathin sections of bulk material has not become an established method. The major limitations are due to the difficulty of achieving the vitrification of such material, and the structural deformation caused by ultrathin sectioning: 1. The vitrification of cells in a physiological environment requires high-pressure freezing. However, new results suggest that the pressure may alter the ultrastructure of the sample. 2. …

Electro-Optical Imaging Of F-Actin And Endoplasmic Reticulum In Living And Fixed Plant Cells, Nina Stromgren Allen, Marty N. Bennett

Scanning Microscopy

Confocal and video micrographs of living and fixed alfalfa roots, onion epithelial and pear pollen cells illustrate the architecture of the cytoskeleton and endoplasmic reticulum in plant cells. Fixation of plant tissues to preserve cytoplasmic structure poses special problems. When possible, emphasis should be placed on the imaging of structures in stained living cells over time. The early events that occur when Nod factors or bacteria elicit nodule formation in alfalfa roots will illustrate several approaches to plant cell fixation, staining and imaging. The first observable events after Nod factor stimulation occur in root hairs and are changes in rates …

Insights, Winter, 1996, Utah State University

Discovery Magazine

Bi-annual alumni newsletter for the College of Science of Utah State University in Logan.

A Scanning Electron Microscopy Study Of Taxus Leaves As Related To Taxonomy, G.A. Strobel, W. M. Hess

Scanning Microscopy

Scanning electron microscopy, when applied to the surfaces of the needles of Taxus spp. (yew) revealed features that appear useful in the taxonomy of this tree species which yields the important anticancer drug, taxol. For instance, all of the four North American species have 3-5 rows of stomata on one-half of the abaxial leaf surface, whereas all of the others, including those from Europe and Asia, have 7-10 rows of stomata. The appearance of individual or fused papilliform epidermal cells and their arrangement on the leaf surface also is a feature that varies between species. Patterns of wax formation appeared …

Preliminary Evaluation Of The Effects Of A Pumping Well On Existing Surface Water Resources Located In T. 12n, R. 2e, Sec. 23, Cache And Box Elder Counties, Denny J. Johnson, Richard C. Peralta

Civil and Environmental Engineering Faculty Publications

This report contains the results of a preliminary study of the impact of pumping a well located in T. 12N, R. 2E, sec. 23, Cache and Box Elder Counties, Utah. A semianalytical capture zone analysis was performed to determine if pumping at the well is likely to reduce flow in Willow Creek or any of three springs in the surrounding area. The well has been used from 1974 to present and is sometimes pumped at 90 gallons per minute (gpm) (verbal communication, Veibell, 1996).

The Chromatin Structure Of Well-Spread Demembranated Human Sperm Nuclei Revealed By Atomic Force Microscopy, M. J. Allen, E. M. Bradbury, R. Balhorn

Scanning Microscopy

The fundamental structure formed when genomic DNA is packaged by protamine in the human sperm nucleus still remains essentially unresolved. It is known that the binding of protamine, a small arginine-rich protein, to DNA generates a large dense, hydrophobic complex making the sperm chromatin structure difficult to study microscopically. To visualize the internal nuclear structures, isolated human sperm nuclei were swollen extensively in saline buffer using only a reducing agent. The nuclei were swollen during deposition onto coverglass and then imaged in the atomic force microscope (AFM). The two main results obtained from imaging individual well-spread nuclei indicate that native …

Defining Arealistic Control For The Chloroform Fumigation-Incubation Method Using Microscopiccounting And 14c-Substrates, William R. Horwath, Eldor A. Paul, David Harris, Jeanette M. Norton, Leslie Jagger, Kenneth A. Horton

Plants, Soils, and Climate Faculty Publications

Chloroform fumigation-incubation (CFI) has made possible the extensive characterization of soil microbial biomass carbon (C) (MBC). Defining the non-microbial C mineralized in soils following fumigation remains the major limitation of CFI. The mineralization of non-microbial C during CFI was examined by adding ¹⁴C-maize to soil before incubation. The decomposition of the ¹⁴C-maize during a 10-d incubation after fumigation was 22.5% that in non-fumigated control soils. Re-inoculation of the fumigated soil raised ¹⁴C-maize decomposition to 77% that of the unfumigated control. A method was developed which varies the proportion of mineralized C from the unfumigated soil …

Atomic Force Microscopy Of Humic Acids, A. Ikai, R. Osterberg

Scanning Microscopy

Atomic force microscopic (AFM) images of humic acids show discrete, globular particles, where particles of the order of magnitude 100 to 300 nm dominate the image fields; the humic acids had been grown to a steady state at pH 5.0. The AFM data are consistent with our previously reported small-angle neutron scattering (SANS) study done under similar conditions. In further agreement, the cluster-cluster interactions shown in our previous SANS study may have their counterparts in closely interacting particles appearing as twin particles in the AFM images.

Preparation Of Cultured Smooth Muscle Cells From Human Myometrium For X-Ray Microanalysis, Jarin Hongpaisan, Godfried M. Roomans

Scanning Microscopy

Methodological aspects of the use of X-ray microanalysis in physiological and pharmacological experiments on cultured myometrial cells were investigated. Cultured human myometrial cells were grown from biopsies after detaching the fibroblasts. Of the cultured cells, 95-98% showed desmin-like immunoreactivity. Transmission electron microscopy showed that subcultured cells were different from myometrial cells in situ. The effects of washing the cells to remove external salt-rich medium were investigated. All solutions removed the external medium, resulting in lower concentrations of Na and Cl. In the cells washed with 0.3 M mannitol, most of the elemental concentrations were significantly lower than in their …

Morphological And Chemical Properties Of Plastic Residues In Composts, Charles R. Krause, Leona E. Horst, Harry A. J. Hoitink

Scanning Microscopy

The relative quantity of plastic film residues and other man-made materials in composts prepared from municipal solid wastes (MSW), biosolids, yard wastes, and pine bark was evaluated utilizing light and scanning electron microscopy equipped with energy dispersive X-ray analyzer. MSW composts screened through a 4 mm screen contained significant but highly variable quantities of plastic film residues and other man-made materials that escaped detection with the unaided eye. The other composts were free of such particles. We conclude that the database for evaluation of man-made materials in MSW composts is inadequate and must be developed further.

Relative Intranuclear Magnesium And Phosphorus Contents In Normal And Tumor Cells Of The Human Thyroid Gland As Revealed By Energy-Dispersive X-Ray Microanalysis, Geza L. Lukacs, Imre Zs.-Nagy, Janos Steiber, Ferenc Gyori, Gyorgy Balazs

Scanning Microscopy

Energy dispersive X-ray microanalysis was performed on altogether 42 surgically removed tissue specimens of 32 patients, which were taken either from intact thyroid parts or various histopathologically verified tumors of the thyroid gland. The tissue specimens were processed with the freeze-fracture-freeze-drying technique and then analyzed in the so-called bulk specimen form. The studies were carried out during the years 1980-81, when intranuclear monovalent ionic composition was studied in detail. From the retained total elemental peak list, it was possible to calculate retrospectively the relative intranuclear Mg and P contents. The data processed by nested (hierarchical) analysis of variance show that …

Imaging The Electrocyte Of Torpedo Marmorata By Scanning Force Microscopy, L. I. Pietrasanta, A. Schaper, G. Q. Fox, F. J. Barrantes, T. M. Jovin

Scanning Microscopy

Scanning force microscopy (SFM) and scanning electron microscopy (SEM) were used to examine the tissue structure of the electric organ of Torpedo marmorata in air and in liquid after applying fracturing and cryosectioning techniques and chemical fixation. The electric organ is organized in columns of stacked electrocytes, arranged in a honeycomb pattern. The columns were cut along a plane normal to the cell stack and thin sections were transferred to polylysine coated glass coverslips. The polarity of the electrocytes was made apparent by immunofluorescence microscopy directed to different domains of the acetylcholine receptor (AChR), thus revealing the innervated face of …

Paleomicrobiological Study In Dental Calculus: Streptococcus Mutans, A. Linossier, M. Gajardo, J. Olavarria

Scanning Microscopy

Morphological types of bacterial remains preserved in ancient tartar of teeth from extinct human groups, which included some communities of coastal gatherers, fishermen, hunters, and farmers, and those practicing a mixed economy, were analyzed. Previous studies have shown the presence of bacteria in ancient tartar. The aim of this work was to determine whether Streptococcus mutans was present in ancient populations (500-12,000 years old). Teeth samples were from ancient skulls obtained from different anthropological collections: the north and south of Chile (before the Spanish conquest), Palencia, Spain, and an eastern Mediterranean region (Levant). Optical microscopy showed Gram positive and Gram …

Hair Bundle Morphology On Surviving Hair Cells Of The Chick Basilar Papilla Exposed To Intense Sound, J. S. Erulkar, D. A. O'Brien, J. C. Saunders

Scanning Microscopy

Exposure to intense sound produces a well-defined "patch" lesion on the chick basilar papilla in which 30-35% of the short hair cells are lost. The present study compares various aspects of sensory hair bundle morphology on surviving hair cells in the patch lesion with hair bundles from matched locations on nonexposed control papilla immediately after removal from the exposure and 12-days post exposure. The height and thickness of the hairs, the total number of hairs in the bundle, the width of the bundle, and the area and perimeter of the apical surface of the hair cell were quantified from scanning …

Video Rate Confocal Laser Scanning Reflection Microscopy In The Investigation Of Normal And Neoplastic Living Cell Dynamics, Pavel Vesely, Alan Boyde

Scanning Microscopy

The introduction of video rate confocal laser scanning microscopes (VRCLSM) used in reflection mode with high magnification, high aperture objective lenses and with further magnification by a zoom facility allowed the first detailed observations of the activity of living cytoplasm and offered a new tool for investigation of the structural transition from the living state to the specimen fixed for electron microscopy (EM). We used a Noran Odyssey VRCLSM in reflection (backscattered) mode. A greater degree of oversampling and more comfortable viewing of the live or taped video image was achieved at zoom factor 5, giving a display monitor field …

Secondary Electron Emission From Simple Metals: Comparative Studies For Al, Mg, And Be, M. Rosler

Scanning Microscopy

In the secondary electron emission (SEE) from solids, the role of different excitation processes is now as ever of special interest from both the theoretical and the experimental points of view. Depending on the primary energy, the relative importance of different excitation mechanisms related to conduction as well as core electrons will be discussed for different simple metals. So far, first principles results are available only for Al for primary energies up to 10 keV. Starting from a microscopic description of the SEE based on the transport equation formalism, calculations were performed for other nearly-free-electron metals (Mg, Be) up to …

Deposition Of Supercoiled Dna On Mica For Scanning Force Microscopy Imaging, B. Samori, I. Muzzalupo, G. Zuccheri

Scanning Microscopy

The deposition of DNA molecules on mica is driven and controlled by the ionic densities around DNA and close to the surface of the substrate. Dramatic improvements in the efficiency and reproducibility of DNA depositions were due to the introduction of divalent cations in the deposition solutions. The ionic distributions on DNA and on mica determine the mobility of adsorbed DNA molecules, thus letting them assume thermodynamically equilibrated conformations, or alternatively trapping them in non-equilibrated conformations upon adsorption.

With these prerequisites, mica does not seem like an inert substrate for DNA deposition for microscopy, and its properties greatly affect the …

Simultaneous Identification Of A Specific Gene Protein Product And Transcript Using Combined Immunocytochemistry And In Situ Hybridization With Non-Radioactive Probes, Gwen V. Childs

Scanning Microscopy

Simultaneous identification of messenger RNA (mRNA) and proteins in the same cells or tissues is a valuable tool to help the cell biologist evaluate the cell secretory cycle. Some cells may produce the mRNA and delay the production of the proteins. Alternatively, the proteins may be rapidly secreted. Other cells may produce both in sequence within the same time frame. Because of this difference, some cells can only be identified by their mRNA product. Others may have both products. This presentation describes a non-radioactive approach to the detection of both products with dual-peroxidase labeling protocols in use in this laboratory …

Electrical Characterization Of Submicrometer Silicon Devices By Cross-Sectional Contact Mode Atomic Force Microscopy, P. De Wolf, T. Trenkler, T. Clarysse, M. Caymax, W. Vandervorst, J. J. Snauwaert, L. Hellemans

Scanning Microscopy

Two contact mode atomic force microscopic (AFM) techniques under ambient conditions are presented for the electrical evaluation of cross sectioned silicon devices. In the first technique, a conductive AFM tip is used as a voltage probe to determine the local potential distribution on the cross section of a silicon device under operation. The electrical potential is measured simultaneously with the surface topography with nanometer resolution and mV accuracy, offering an easy way of correlating topographic and electrical features. A second method, nanometer spreading resistance profiling (nano-SRP), performs localized spreading resistance measurements to determine the spatial distribution of charge carriers in …