Digital Commons Network^™

Hydrogeomorphic Segments And Hydraulic Microhabitats Of The Niobrara River, Nebraska, With Special Emphasis On The Niobrara National Scenic River, Jason S. Alexander, Ronald B. Zelt, Nathaniel J. Schaepe

United States Geological Survey: Water Reports and Publications

The Niobrara River is an ecologically and economically important resource in Nebraska. The Nebraska Department of Natural Resources’ recent designation of the hydraulically connected surface- and groundwater resources of the Niobrara River Basin as “fully appropriated” has emphasized the importance of understanding linkages between the physical and ecological dynamics of the Niobrara River so it can be sustainably managed. In cooperation with the Nebraska Game and Parks Commission, the United States Geological Survey USGS) investigated the hydrogeomorphic and hydraulic attributes of the Niobrara River in northern Nebraska. This report presents the results of an analysis of hydrogeomorphic segments and hydraulic …

The Escherichia Coli K-12 Orfeome: A Resource For Comparative Molecular Microbiology, Seesandra V. Rajagopala, Natsuko Yamamoto, Adrienne E. Zweifel, Tomoko Nakamichi, Hsi-Kuang Huang, Jorge David Mendez-Rios, Jonathan Franc-Koh, Meher Preethi Boorgula, Kazutoshi Fujita, Ken-Ichirou Suzuki, James C. Hu, Barry L. Wanner, Hirotada Mori, Peter Uetz

Department of Biological Sciences Faculty Publications

Background

Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput fashion.

Results

We have constructed an open reading frame (ORFeome) collection of 3974 or 94% of the knownEscherichia coli K-12 ORFs in Gateway^® entry vector pENTR/Zeo. The collection has been used for protein expression and protein interaction studies. For example, we have compared interactions among YgjD, YjeE and YeaZ proteins in E. coli, Streptococcus pneumoniae, and …

Primary Human Mammary Epithelial Cells Endocytose Hiv-1 And Facilitate Viral Infection Of Cd4+ T Lymphocytes, Stephanie M. Dorosko, Ruth I. Connor

Dartmouth Scholarship

The contribution of mammary epithelial cells (MEC) to human immunodeficiency virus type 1 (HIV-1) in breast milk remains largely unknown. While breast milk contains CD4(+) cells throughout the breast-feeding period, it is not known whether MEC directly support HIV-1 infection or facilitate infection of CD4(+) cells in the breast compartment. This study evaluated primary human MEC for direct infection with HIV-1 and for indirect transfer of infection to CD4(+) target cells. Primary human MEC were isolated and assessed for expression of HIV-1 receptors. MEC were exposed to CCR5-, CXCR4- and dual-tropic strains of HIV-1 and evaluated for viral reverse transcription …

Low-Loss Hollow Waveguide Platforms For Optical Sensing And Manipulation, Evan J. Lunt

Theses and Dissertations

This dissertation presents a method for fabricating integrated hollow and solid optical waveguides on planar substrates. These waveguides are antiresonant reflecting optical waveguides (ARROWs), where high-index cladding layers confine light to hollow cores through optical interference. Hollow waveguides that can be filled with liquids or gases are an important new building block for creating highly-integrated optical sensors. The method developed for fabricating these integrated waveguides employs standard processes and materials used in the microelectronics industry, allowing for parallel, low-cost fabrication. Dielectric cladding layers are deposited on a silicon wafer using plasma-enhanced chemical vapor deposition (PECVD). After the lower cladding layers …

O/Oreos Nanosatellite: A Multi-Payload Technology Demonstration, Giovanni Minelli, Antonio Ricco, Christopher Beasley, John Hines, Elwood Agasid, Bruce Yost, David Squires, Charlie Friedericks, Matthew Piccini, Greg Defouw, Mike Mcintyre, Robert Ricks, Macarena Parra, Millan Diaz-Aguado, Linda Timucin, Mike Henschke, Matthew Lera, Ming Tan, Mike Cohen, Karolyn Ronzano, Ed Luzzi, Nghia Mai, Aaron Schooley, Dianna Ly, Eric Stackpole, Jeffrey Lin, John Tucker, Pascale Ehrenfreund, Nathan Santos, Bramall, Kathryn Bryson, Julie Chittenden, Cindy Taylor, Amanda Cook

Small Satellite Conference

The Organism/Organic Exposure to Orbital Stresses (O/OREOS) nanosatellite follows in the footsteps of the successful GeneSat-1 and PharmaSat missions to validate key technologies developed to conduct compelling science experiments in space for a small price tag. Developed by the Small Spacecraft Division at NASA Ames Research Center, the 5.5-kg 3U satellite contains two completely independent payloads and a novel drag-enhancing device which shortens the spacecraft’s orbital lifetime, thereby mitigating orbital debris. This paper provides an overview of the mission as well as an in-depth discussion of each payload and the de-orbit mechanism (DOM) while highlighting lessons learned from the spacecraft’s …

Knowing Your Community: Fostering Biodiversity Awareness In Our Students’ Daily Existence, Tony Cummings Bs, Academic Director

Fostering Multicultural Competence and Global Justice: an SIT Symposium

There are strong arguments suggesting that developing students’ sensitivity to local biodiversity and conservation issues is as important as emphasizing an understanding of global conservation issues happening in faraway lands (Ehrenfeld, 2009). Many students arrive at a Study Abroad destination, with a good understanding of theory, but with little field experience at home. Environmental educators in Study Abroad are able to use the novelty and grandeur of our exotic destinations to systematically teach students the patterns and processes of ecological and human communities at our sites, while inspiring a sense of place in our students. By immersing students in the …

Environmental Sustainability: Challenges And Opportunities Of Greening Your Study Abroad Program, Sylvia M. Seger Mim, Academic Director

Fostering Multicultural Competence and Global Justice: an SIT Symposium

World Learning’s mission to “… create a more peaceful and just world” by necessity encompasses environmental dynamics, considering that the root causes of most social justice issues and violent conflicts can be traced to environmental degradation and disproportional access to shrinking natural resources. Thus our mission mandates that we employ an ethic of environmental stewardship in all our pursuits and put in place mechanisms to mitigate our environmental impacts.

“We shall never achieve harmony with land, any more than we shall achieve absolute justice or liberty for people. In these higher aspirations, the important thing is not to achieve but …

Olfar, A Radio Telescope Based On Nano-Satellites In Moon Orbit, S. Engelen, C.J.M. Verhoeven, M.J. Bentum

Small Satellite Conference

It seems very likely that missions with nano-satellites in professional scientific or commercial applications will not be single-satellite missions. Well structured formations or less structured swarms of nano-satellites will be able to perform tasks that cannot be done in the “traditional” way. The Dutch space-born radio telescope project OLFAR, the Orbiting Low Frequency Array, is a good example of a typical “swarm-task”. The OLFAR radio telescope will be composed of an antenna array based on nano-satellites orbiting the moon to shield the receiving nodes from terrestrial interference. The array will receive frequencies in a band from around 30 kHz to …

Study Of The Small: Potential For Operational Military Use Of Cubesats , Chalie Galliand

Small Satellite Conference

The DoD is known for looking to innovative thinking to provide answers to it warfighter’s needs. This holds very true in the realm of space based capabilities. Recently, the sizes of assets in space have been shrinking in size. However, their capabilities have been growing at an accelerated rate. CubeSats are quickly becoming an area of interest because of their growing potential to fulfill operational military missions.

G-Lattices For An Unrooted Perfect Phylogeny, Monica Grigg

Mathematical Sciences Technical Reports (MSTR)

We look at the Pure Parsimony problem and the Perfect Phylogeny Haplotyping problem. From the Pure Parsimony problem we consider structures of genotypes called g-lattices. These structures either provide solutions or give bounds to the pure parsimony problem. In particular, we investigate which of these structures supports an unrooted perfect phylogeny, a condition that adds biological interpretation. By understanding which g-lattices support an unrooted perfect phylogeny, we connect two of the standard biological inference rules used to recreate how genetic diversity propagates across generations.

A Perturbation Method For Inference On Regularized Regression Estimates, Jessica Minnier, Lu Tian, Tianxi Cai

Harvard University Biostatistics Working Paper Series

No abstract provided.

Aspergillus Fumigatus Sida Is A Highly Specific Ornithine Hydroxylase With Bound Flavin Cofactor, Samuel W. Chocklett, Pablo Sobrado

Chemistry Faculty Research & Creative Works

Ferrichrome is a hydroxamate-containing siderophore produced by the pathogenic fungus Aspergillus fumigatus under iron-limiting conditions. This siderophore contains N5-hydroxylated l-ornithines essential for iron binding. A. fumigatus siderophore A (Af SidA) catalyzes the flavin- and NADPH-dependent hydroxylation of l-ornithine in ferrichrome biosynthesis. Af SidA was recombinantly expressed and purified as a soluble tetramer and is the first member of this class of flavin monooxygenases to be isolated with a bound flavin cofactor. The enzyme showed typical saturation kinetics with respect to l-ornithine while substrate inhibition was observed at high concentrations of NADPH and NADH. Increasing amounts of hydrogen peroxide were measured …

Kinetic And Spectroscopic Studies Of Hemin Acquisition In The Hemophore Hasap From Pseudomonas Aeruginosa, Erik T. Yukl, Grace Jepkorir, Aileen Y. Alontaga, Lawrence Pautsch, Juan C. Rodriguez, Mario Rivera, Pierre Moënne-Loccoz

Faculty Publications

The extreme limitation of free iron has driven various pathogens to acquire iron from the host in the form of heme. Specifically, several Gram-negative pathogens secrete a heme binding protein known as HasA to scavenge heme from the extracellular environment and to transfer it to the receptor protein HasR for import into the bacterial cell. Structures of heme-bound and apo-HasA homologues show that the heme iron(III) ligands, His32 and Tyr75, reside on loops extending from the core of the protein and that a significant conformational change must occur at the His32 loop upon heme binding. Here, we investigate the kinetics …

Florida Sentinel Bulletin, August 10, 2010, Gwen Hayes

Florida Sentinel Bulletin Collection

The August 10, 2010, issue of the Florida Sentinel Bulletin.

Method For Determining The Specific Growth Rate Of Distinct Microbial Populations In A Non-Homogeneous System, Peter George Stroot, Matthew Raymond Cutter, Samuel James Dupont, Jr.

USF Patents

The present invention pertains to a molecular biology-based method and kit for measuring the specific growth rate (or cell doubling time) of distinct microbial populations. The method and kit can be used to analyze mixed culture samples that have been exposed to chloramphenicol or other protein synthesis inhibitors for defined times. In a preferred embodiment, the method of the invention (also referred to herein as FISH-RiboSyn) is an in situ method that utilizes fluorescence in situ hybridization (FISH) with probes that target: (1) the 5′ or 3′ end of precursor 16S rRNA; or (2) the interior region of both precursor …

Glaucoma Treatment Breakthrough

News Releases

No abstract provided.

Incorporating Genomics And Bioinformatics Across The Life Sciences Curriculum, Jayna L. Ditty, Christopher A. Kvaal, Brad Goodner, Sharyn K. Freyermuth, Cheryl Bailey, Robert A. Britton, Stuart G. Gordon, Sabine Heinhorst, Kelyenne Reed, Zhaohui Xu, Erin R. Sanders-Lorenz, Seth Axen, Edwin Kim, Mitrick Johns, Kathleen Scott, Cheryl A. Kerfeld

Faculty Publications

No abstract provided.

Utilization Of Pleurotus Sajor-Caju Stalks As Feed Supplement In Diet Of Juvenile Oreochromis Niloticus (Tilapia) / Thenamutha Muniandy, Thenamutha Muniandy

Student Works (2010-2019)

In this study, the potential use of the powdered Pleurotus sajor caju (Oyster mushroom) stalks as a supplemented feed for juvenile Oreochromis niloticus was evaluated by observing the growth level(length, body weight and specific growth rate (SGR), survival and also by measuring the water quality parameters (pH, temperature, Ammonia, Nitrite, Nitrate and dissolved oxygen). Stalks of P. sajor-caju are a waste product from the mushroom industry which is known to be an economical, abundant and good protein source. Diets were incorporated with commercial feed in proportion of P. sajor-caju25% (Diet1), P. sajor-caju50% (Diet2) and control feed(Diet3). The survival of O. …

Role Of Ampk In The Upregulation Of Steroidogenic Acute Regulatory Protein In The Zona Fasciculata Of The Adrenal Cortex, Adam Wesley Dayton

Theses and Dissertations

Cortisol is a glucocorticoid produced by the zona fasciculata (ZF) of the adrenal cortex. Traditionally, cortisol production and release was seen as being regulated strictly by adrenocorticotropic hormone (ACTH). While this is true of baseline cortisol levels and in response to acute mental stress, the picture is somewhat more complicated in other situations.Interleukin-6 (IL-6) contributes to the maintenance of cortisol levels in situations of prolonged immune or inflammatory stress. AMP activated protein kinase (AMPK) was investigated as a possible mediator of the action of IL-6 or as an independent actor in raising cortisol levels in response to hypoxemic or hypoglycemic …

Invasive Predators Deplete Genetic Diversity Of Island Lizards, Amandine Gasc, M. C. Duryea, Robert M. Cox, Andrew Kern, Ryan Calsbeek

Dartmouth Scholarship

Invasive species can dramatically impact natural populations, especially those living on islands. Though numerous examples illustrate the ecological impact of invasive predators, no study has examined the genetic consequences for native populations subject to invasion. Here we capitalize on a natural experiment in which a long-term study of the brown anole lizard (Anolis sagrei) was interrupted by rat invasion. An island population that was devastated by rats recovered numerically following rat extermination. However, population genetic analyses at six microsatellite loci suggested a possible loss of genetic diversity due to invasion when compared to an uninvaded island studied over …

Radially Aligned, Electrospun Nanofibers As Dural Substitutes For Wound Closure And Tissue Regeneration Applications, Jingwei Xie, Matthew R. Macewan, Wilson Z. Ray, Wenying Liu, Daku Y. Siewe, Younan Xia

MIIR Faculty Research

This paper reports the fabrication of scaffolds consisting of radially aligned poly(ε-caprolactone) nanofibers by utilizing a collector composed of a central point electrode and a peripheral ring electrode. This novel class of scaffolds was able to present nanoscale topographic cues to cultured cells, directing and enhancing their migration from the periphery to the center. We also established that such scaffolds could induce faster cellular migration and population than nonwoven mats consisting of random nanofibers. Dural fibroblast cells cultured on these two types of scaffolds were found to express type I collagen, the main extracellular matrix component in dural mater. The …

Pismo Beach Fecal Contamination Source Identification Study: Final Report, Christopher L. Kitts, Michael W. Black, Mark M. Moline, Marie Yeung, Alice K. Hamrick, Ian C. Robbins, Andrew A. Schaffner, Nathania I. Boutet

Biological Sciences

No abstract provided.

Woods V. Sanders Appellant's Reply Brief Dckt. 37483

Idaho Supreme Court Records & Briefs, All

No abstract provided.

Formation Of Complex And Unstable Chromosomal Translocations In Yeast, Kristina H. Schmidt, Emilie Viebranz, Lillian Doerfler, Christina Lester, Aaron Rubenstein

Molecular Biosciences Faculty Publications

Genome instability, associated with chromosome breakage syndromes and most human cancers, is still poorly understood. In the yeast Saccharomyces cerevisiae, numerous genes with roles in the preservation of genome integrity have been identified. DNA-damage-checkpoint-deficient yeast cells that lack Sgs1, a RecQ-like DNA helicase related to the human Bloom's-syndrome-associated helicase BLM, show an increased rate of genome instability, and we have previously shown that they accumulate recurring chromosomal translocations between three similar genes, CAN1, LYP1 and ALP1. Here, the chromosomal location, copy number and sequence similarity of the translocation targets ALP1 and LYP1 were altered to gain insight into the …

August 9, 2010 Reporter, University Of Alabama At Birmingham

eReporter (campus newsletter)

No abstract provided.

Overview Of Learning Theories (Chapter 1 Of Faith-Based Education That Constructs), Debra S. Espinor

Faculty Publications - College of Education

Virtually everyone would agree that the role of the school is to help students learn. The school, as an institution of education, must incorporate a sense of morality or values. This said, the methods of incorporating morality and values into education vary. This chapter explores three of the most common learning theories of the last fifty years: behaviorism, cognitivism, and constructivism. Each section will take a brief glance at the history, background, and definition of each of the theories. Then, the chapter will turn to the strengths and weaknesses of each of the theories, illuminating their role in supporting students' …

Variability In Avian Eggshell Colour: A Comparative Study Of Museum Eggshells, Phillip Cassey, Steven J. Portugal, Golo Maurer, John G. Ewen, Rebecca L. Boulton, Mark E. Hauber, Tim M. Blackburn

Publications and Research

Background The exceptional diversity of coloration found in avian eggshells has long fascinated biologists and inspired a broad range of adaptive hypotheses to explain its evolution. Three main impediments to understanding the variability of eggshell appearance are: (1) the reliable quantification of the variation in eggshell colours; (2) its perception by birds themselves, and (3) its relation to avian phylogeny. Here we use an extensive museum collection to address these problems directly, and to test how diversity in eggshell coloration is distributed among different phylogenetic levels of the class Aves. Methodology and Results Spectrophotometric data on eggshell coloration were collected …

Variable Palatability Of Quaking Aspen For Large Ungulate Herbivores, Patrice Alexa Nielson

Theses and Dissertations

Aspen is a key resource in the Rocky Mountain Region for wildlife forage and habitat, lumber products, scenery, and plays important roles in fire ecology and hydrological processes. There is evidence of aspen decline over much of the Intermountain West for approximately 100 years. In Dixie and Fishlake National Forests, UT, aspen distribution has decreased by nearly half. Causes of this decline are not well understood, although wildlife browsing by ungulates has been implicated as playing a major role. The objective of this research was to examine what soil or plant factors might be involved in wildlife browse choice in …

The Design Of Specifications For The Development Of Broadcast English Materials In Academic Listening/Speaking Courses, Amy Barlow

Theses and Dissertations

ESL students in academic listening/speaking courses often listen to long audio recordings similar to a lecture or other academic passages. When listening to these passages, students can lose their interest which impedes their learning of new strategies for understanding academic language. Students in the Level Four Listening/Speaking classes at Brigham Young University's English Language Center (ELC), under the previous curriculum, would experience this challenge. All of the passages were available only in audio and were long in duration. The students would lose interest and improve little in their listening skills. Under the new curriculum at the ELC, students in Academic …

A Detailed Phylogenetic Analysis Of Fiv In The United States, Eric A. Weaver

School of Biological Sciences: Faculty Publications

Background: Feline immunodeficiency virus (FIV) is a lentivirus associated with AIDS-like illnesses in cats and has been used as a model for the study of human immunodeficiency virus (HIV). A feature of HIV and FIV infection is the continually increasing divergence among viral isolates between different individuals, as well as within the same individuals.

Methodology/Principal Findings: The goal of this study was to determine the phylogenetic patterns of viral isolates obtained within the United States (U.S.) by focusing on the variable, V3-V4, region of the FIV envelope gene.

Conclusions/Significance: Data indicate that FIV, from within the U.S., localize to four …