Digital Commons Network^™

The Effect Of Ocean Acidification On The Growth Rate And Metabolic Activity Of Various Vibrio Species, Mireya Arroyo

McNair Scholars Research Journal

No abstract provided.

Molecular Signal Adaptations Caused By Cocaine, Conditioned Reward, And Estrogen, Sarah K. Anderson

McNair Scholars Research Journal

No abstract provided.

Role Of Reverse Transcriptase Domain 0 In Non-Ltr Retrotransposon Integration, Jeremy D. Cortez

McNair Scholars Research Journal

No abstract provided.

Full Issue, The Mcnair Team

McNair Scholars Research Journal

No abstract provided.

Dual Capture Of A Piñon Deer Mouse And A Silky Pocket Mouse Resulting In Consumption Of The Smaller Animal, Jon C. Pigage, Roger D. Peyton

The Prairie Naturalist

Intraspecific dual captures of rodents are uncommon, but not rare. There are several reports of brown rats (Rattus norvegicus), white-footed deer mice (Peromyscus leucopus), North American deer mice (P. maniculatus), western harvest mice (Reithrodontomys megalotis) and meadow voles (Microtus pennsylvanicus) caught simultaneously in the same trap (i.e. a door-closing live-trap; Davis 1955, Getz 1961, Blaustein and Rothstein 1978, Jenkins and Llewellyn 1981, Novak 1983). Some reports are incidental whereas others are interpreted as social associations or bonding between conspecifics. Interspecific dual captures are rarely reported in the literature. The earliest report of …

A Simple Device For Measuring The Minimum Current Velocity To Maintain Semi-Buoyant Fish Eggs In Suspension, Julias S. Mueller, Brandon D. Cheek, Qingman Chen, Jillian Groeschel, Shannok K. Brewer, Timothy B. Grabowski

The Prairie Naturalist

Pelagic broadcast spawning cyprinids are common to Great Plains rivers and streams. This reproductive guild produces non-adhesive semi-buoyant eggs that require sufficient current velocity to remain in suspension during development. Although studies have shown that there may be a minimum velocity needed to keep the eggs in suspension, this velocity has not been estimated directly nor has the influence of physicochemical factors on egg buoyancy been determined. We developed a simple, inexpensive flow chamber that allowed for evaluation of minimum current velocity needed to keep semi-buoyant eggs in suspension at any time frame during egg development. The device described here …

Red-Tailed Hawk Nesting In Kansas: Influence Of Landscape Characteristics, William Langley

The Prairie Naturalist

Factors that affect nest site selection in red-tailed hawks (Buteo jamaicensis) include the physical features surrounding the nest and landscape characteristics. Features surrounding nests include: tree height, tree diameter (dbh), percent canopy cover, slope, nest openness, and density of woody plants or shrubs (Titus and Mosher 1981, Bechard et al. 1990, Tietje et al. 1997, Actkinson et al. 2007). Landscape characteristics that influence nest-site selection by red-tailed hawks vary across regions. In Georgia, red-tailed hawks selected nest site in areas with greater area of agriculture and open pasture (Moorman and Chapman 1996), whereas in Oklahoma prairies, the hawks …

Use Of Seeded Exotic Grasslands By Wintering Birds, Andrew D. George, Timothy J. O'Connell, Karen R. Hickman, David M. Lesliee Jr.

The Prairie Naturalist

Despite widespread population declines of North American grassland birds, effects of anthropogenic disturbance on wintering habitat of this guild remain poorly understood. We compared avian abundance and habitat structure in fields planted to the exotic grass Old World bluestem (Bothriochloa ischaemum; OWB) to that in native mixed-grass prairie. During winters of 2007–2008 and 2008–2009, we conducted bird and vegetation surveys in six native grass and six OWB fields in Garfield, Grant, and Alfalfa counties, Oklahoma. We recorded 24 species of wintering birds in native fields and 14 species in OWB monocultures. While vegetation structure was similar between field …

Whooping Cranes Consume Plains Leopard Frogs At Migratory Stopover Sites In Nebraska, Keith Geluso, Brad T. Krohn, Mary J. Harner, Michael J. Assenmacher

The Prairie Naturalist

Whooping cranes (Grus americana) currently consist of a single, wild population that migrates annually from breeding grounds at Wood Buffalo National Park, Canada, to wintering grounds on and around the Aransas National Wildlife Refuge along the Texas coast, USA (NRC 2005). This population reached a low of less than 20 individuals in 1941 (Allen 1952) but has rebounded to over 250 individuals (Chavez-Ramirez and Wehtje 2012, Gil-Weir et al. 2012). Whooping cranes migrate approximately 4,000 km each spring and autumn, traversing much of the North American Great Plains (Lewis 1995) and periodically landing along rivers, wetlands, and other …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New CRAN task views

New packages in CRAN task views

New contributed packages

Other changes

News From The Bioconductor Project, Bioconductor Team

The R Journal

Bioconductor 2.13 was released on 15 October2013. It is compatible with R3.0.2, and consists of 749 software packages, 179 experiment data packages, and more than 690 up-to-date annotation packages. The release includes 84 new software packages, and enhancements to many others. Descriptions of new packages and updated NEWS files provided by current package maintainers are at http://bioconductor.org/news/bioc_2_13_release/

Surface Melting Curve Analysis With R, Stefan Rödiger, Alexander Böhm, Ingolf Schimke

The R Journal

Nucleic acid Melting Curve Analysis is a powerful method to investigate the interaction of double stranded nucleic acids. Many researchers rely on closed source software which is not ubiquitously available, and gives only little control over the computation and data presentation. R in contrast, is open source, highly adaptable and provides numerous utilities for data import, sophisticated statistical analysis and presentation in publication quality. This article covers methods, implemented in the MBmca package, for DNA Melting Curve Analysis on microbead surfaces. Particularly, the use of the second derivative melting peaks is suggested as an additional parameter to characterize the melting …

The Effects Of Isolation On Endemic Cozumel Island Rodents: A Test Of The Island Rule, Brittany Marie Nuttall

Theses and Dissertations

Island isolation can cause changes in body size, cranial characteristics, and genetic variation in mammals. We use geometric morphometrics to test skull and mandible shape and size change across three species of endemic Cozumel Island rodents in order to test the “island rule” of larger size in isolated rodents. We also sequenced the D-Loop and cytochrome b region of the mitochondrial genome and tested for differences in genetic variation between island and mainland groups, as well as population structure and gene flow in order to assess the effect of island isolation on these three rodents. We found that the three …

Application Of Next-Generation Transcriptomic Tools For Non-Model Organisms: Gene Discovery And Marker Developmentwithin Plecoptera (Insecta), Nicholas Gregory Davis

Theses and Dissertations

Phylogenetic research on non-model organisms has been hindered by limited marker availability. Next generation sequencing techniques are eliminating that barrier. Using Illumina sequencing technology, Trinity assembly software, custom Perl reciprocal BLAST scripts, and Primer3 primer prediction software, we produced and analyzed 7 Plecopteran transcriptomes, representing 7 of the 16 total families, in an attempt to identify and develop conserved orthologous genetic markers. The transcriptomes were used to reconstruct a gene content phylogeny using a simple distance matrix generated from reciprocal blastn data. By producing and filtering a reciprocal blast network we identified and aligned over 450 putative orthologs. Out of …

Habitat Selection By Two K-Selected Species: An Application To Bison And Sage Grouse, Joshua Taft Kaze

Theses and Dissertations

Population growth for species with long lifespans and low reproductive rates (i.e., K-selected species) is influenced primarily by both survival of adult females and survival of young. Because survival of adults and young is influenced by habitat quality and resource availability, it is important for managers to understand factors that influence habitat selection during the period of reproduction. My thesis contains two chapters addressing this issue for K-selected species in Utah. Chapter one evaluates habitat selection of greater sage-grouse (Centrocercusurophasianus) on Diamond Mountain during the critical nesting and brood-rearing period. Chapter two address selection of birth sites by bison (Bison …

Exploring Post-Fire Recovery Of Biocrusts And Desert Ecosystem Services, Jason R. Bahr

Theses and Dissertations

Biocrusts and the ecosystem services they provide are becoming more susceptible to fire as exotic annual grass invasions facilitate the spread of desert wildfires. Further, precipitation patterns across the western United States are predicted to change over the next century, and have the potential to dramatically influence fire regimes and the recovery of burned biocrusts. Despite these changes to desert fire and precipitation cycles, our understanding of post-fire biocrust recovery is limited, especially regarding the first two years after fire. To investigate biocrust recovery, we created burn manipulations (i.e., unburned and burned) and tracked crust form and function over two …

Importance Of Placement Depth In Evaluating Soil Nitrogen, Phosphorus, And Sulfur Using Ion Exchange Resin Capsules In Semi-Arid, Low Fertility Soils, Rachel Lynn Buck

Theses and Dissertations

Ion exchange resin capsules provide a possible alternative to conventional soil testing procedures. Previous studies with semi-arid, low fertility soils observed poor relationships with poorly mobile nutrients such as phosphorus (P). We propose that placement depth may improve those relationships. Our objective was to (1) determine if placement depth could improve resin capsule estimation of the bioavailability of nitrogen (N), P, and sulfur (S) and (2) to determine if resin capsules can effectively estimate S availability in semi-arid, low fertility soils. Field sites were established in Rush and Skull Valleys, Utah on loam and sandy loam soils, respectively. Fertilizer was …

Involvement Of Ampk And Ap-1 Biochemical Pathways In Il-6 Regulation Of Steroidogenic Enzymes In The Adrenal Cortex, Matharage Shenali De Silva

Theses and Dissertations

The adrenal cortex is a crucial endocrine gland in the mammalian stress response. In chronic inflammatory stress, cortisol is elevated whereas adrenal androgens are decreased. Furthermore, ACTH levels have poor correlation with the plasma cortisol in these conditions, thus suggesting that other factors are driving the stress response during chronic inflammatory stress. Interleukin-6 (IL-6), a cytokine which is released during chronic inflammatory stress, is assumed to be one such factor. Thus the biochemical pathways by which IL-6 increases cortisol release from the zona fasciculata (ZF), and decreases adrenal androgen release from the zona reticularis (ZR) were investigated. Since IL-6 activates …

Ferritin-Based Photo-Oxidation Of Biomass For Nanoparticle Synthesis, Bioremediation, And Hydrogen Evolution, Oscar Petrucci

Theses and Dissertations

The cell is the basic unit of all living organisms. It is an amazing machine capable of self-replicating, growing, and synthesizing and shuttling thousands of compounds. To perform all of these activities the cell needs energy. The original source of energy for all living beings is the Sun. The energy of the sun is collected by the autotrophs (mostly plants) through photosynthesis and stored in the chemical bonds of carbohydrates and lipids through carboxylic acid intermediates; animals use these compounds to obtain the energy for their cells. Most of the energy extracted by the cell comes from the citric acid …

Fgf4 Induced Wnt5a Gradient In The Limb Bud Mediates Mesenchymal Cell Directed Migration And Division, John C. Allen

Theses and Dissertations

The AER has a vital role in directing embryonic limb development. Several models have been developed that attempt to explain how the AER directs limb development, but none of them are fully supported by existing data. I provide evidence that FGFs secreted from the AER induce a gradient of Wnt5a. I also demonstrate that limb mesenchyme grows toward increasing concentrations of Wnt5a. We hypothesize that the changing shape of the AER is critical for patterning the limb along the proximal to distal axis. To better understand the pathway through which Wnt5a elicits its effects, we have performed various genetic studies. …

Analysis Of Energy Flow In Us Globec Ecosystems Using End-To-End Models, James J. Ruzicka, John H. Steele, Sarah K. Gaichas, Tosca Ballerini, Dian J. Gifford, Richard D. Brodeur, Eileen E. Hofmann

Graduate School of Oceanography Faculty Publications

End-to-end models were constructed to examine and compare the trophic structure and energy flow in coastal shelf ecosystems of four US Global Ocean Ecosystem Dynamics (GLOBEC) study regions: the Northern California Current, the Central Gulf of Alaska, Georges Bank, and the Southwestern Antarctic Peninsula. High-quality data collected on system components and processes over the life of the program were used as input to the models. Although the US GLOBEC program was species-centric, focused on the study of a selected set of target species of ecological or economic importance, we took a broader community-level approach to describe end-to-end energy flow, from …

Raman Spectroscopic Investigation Of Chondroitinase Abc Treatment After Spinal Cord Injury In An Organotypic Model, Shane Ruberto

Theses - ALL

This study investigated (1) the ability of an organotypic model of spinal cord injury (SCI) to recapitulate significant pathobiological events of in vivo SCI from a Raman spectroscopic perspective, and (2) the Raman spectroscopic effects of chondroitinase ABC (cABC) treatment on said model of SCI. Tissue from mouse spinal cords was excised, sectioned, and placed into culture, before being systematically injured to induce trauma. Cultures with and without cABC treatment were assessed using Raman spectroscopy at varying times post-injury. We demonstrate that Raman spectral phenomena characteristic of SCI can be observed using an organotypic model. By comparing these phenomena with …

Nature Of Science Conceptions, Attitudes Towards Evolution And Global Climate Change, And Course Achievement In An Introductory Biology Course, Benjamin Elijah Carter

Theses - ALL

Many researchers have studied student attitudes toward and knowledge of evolutionary science, attitudes towards global climate change (GCC), conceptions about the nature of science (NOS), and course success. However, at the time of this writing, no studies explicitly link these topics.

It is overwhelmingly acknowledged by the scientific community that evolution and global climate change (GCC) are undeniably supported by physical evidence. And yet, both topics remain very politically contentious in the United States. Efforts to mitigate the disconnects between the scientific community and the general public on these issues are imperative to science education. Such undertakings need to examine …

Reducing Digestible Tidbits From Meaty Stock: Satisfying Varied Tastes With An Attractive Instructional Assessment Menu, Erika Bennett, Jennie Simning, Kim Staley

LOEX Conference Proceedings 2011

Do you collect streams of data that never see the light of day? Libraries are more frequently being held accountable for metrics via scorecards, dashboards, and other short snapshots of performance. Information Literacy practitioners have meanwhile moved away from tick-marks to a learning outcome assessment culture. This means that the full array of evaluative, formative and summative approaches-- competencies, tests, self-reports and rubrics-- can leave new librarians' heads spinning.

Learning outcomes data are hard to wrangle, let alone, in a digestible format, but fresh assessment approaches can fully illustrate the benefits of our varied media and modes of instruction. Instead …

Influence Of Hydrogel Substrate On Cell Growth And Virus Infection, Fan Yang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The interaction of cells with their extracellular matrix is of great importance when cells adapt to their environment. The purpose of this thesis is to design substrates with controllable properties and to study cellular interaction on these substrates. Firstly, enzymatically cross-linked gelatin hydrogels with different elastic modulus were prepared. Then, we studied the condition of cell growth and virus infection on these hydrogels as a followed-up. In the first part of the study, we made enzymatically cross-linked gelatin hydrogels with five different elastic modulus. As a parameter of stiffness, elastic modulus varies from 2.4 KPa to 7.5 KPa based on …

A Study On Two Optimal Planning Problems In Smart Grid, Eting Yuan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Optimized planning of power devices and power generators is essential for saving energy and reducing costs in smart grid. Many of these optimization problems share a common characteristic and seek to optimize accumulated rewards or costs within a finite time planning horizon. For this reason, some of those problems can be formulated as finite horizon optimal planning problems. This dissertation performs detailed investigation on two representative finite horizon optimal planning problems: the Unit Commitment problem (UCP) and the Voltage and Reactive Power Control (VVC) Problem. UCP is an important optimal power planning problems in electric grids. The purpose of UCP …

Lack Of Csk-Mediated Negative Regulation In A Unicellular Src Kinase, Kira Schultheiss

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Tyrosine kinases play important roles in cellular communication in animals. c-Src is a nonreceptor tyrosine kinase that is involved in survival, angiogenesis, proliferation, and invasion pathways. There are 9 Src family kinases, and they have a conserved domain arrangement (SH3-SH2-kinase) that is necessary for regulation. The basal activity of c-Src is normally kept low due to phosphorylation by C-terminal Src kinase (Csk). This regulatory relationship has been conserved throughout the evolution of animals. Until recently, it was thought that complex signaling molecules, such as the tyrosine kinases, did not exist outside of multicellular animals. Newly discovered unicellular precursors to mammalian …

Reproduction, Sexual Swellings And Mating Behavior In Sanje Mangabeys (Cercocebus Sanjei), David Fernandez Sobrado

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Inter-sexual conflict, or the opposing reproductive strategies of males and females, has become a primary structural factor in current models of social organization as it drives an evolutionary arms-race between the sexes. In many primates living in polygynandrous groups, the mating strategy of dominant males is to guard fertile females, while females develop sexual swellings that provide males with information regarding the approximate, but not exact, timing of ovulation. This allows females to mate promiscuously, confusing paternity, while concentrating paternity on males with the best competitive ability, i.e. | those that are able to mate guard during the peak swelling …

Regulatory Mechanism Of Hematopoietic Stem Cell Self-Renewal By Stem Cell Factor Sall4, Jing Yang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

All types of blood cells in the human body are derived from Hematopoietic Stem Cells (HSCs).The self-renewal ability of HSCs ensure that blood cells replenish and sustain life. The regulatory mechanism of HSCs self-renewal, however, remains an unsolved problem. Recent studies found that the stem cell gene SALL4 has the ability to stimulate HSCs expansion and maintain their pluripotent tendencies. In this article we summarize the current research on SALL4 and its isoforms, and how they affect HSCs self-renewal capacity. To further understand the regulatory mechanism underlying this activity, researchers explored the connection between SALL4 and other regulatory molecules. They …

(I) Synthesis And Application Of Chiral Biphenol-Based Phosphorus Ligands To Catalytic Asymmetric Synthesis; (Ii) Rhodium-Catalyzed Cycloaddition Reactions For Rapid Construction Of Polycyclic Skeletons Of Biological Interest, Chih-Wei Chien

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Chiral ligand design is crucial for the asymmetric transformations. In our laboratory, libraries of fine-tunable phosphorus ligands based on axially chiral biphenol have been well developed. These ligands exhibit excellent enantioselectivity in various transition-metal catalyzed asymmetric reactions. We present here the application of the monodentate phosphoramidite (MPN) ligand library to the Pd-catalyzed intramolecular asymmetric allylic amination (AAA) for the formation of chiral 1-vinyltetrahydroiso-quinoline skeleton, a versatile key intermediate in the synthesis of natural products such as isopyruthaline and (− )-O-methylthaicanine. We also studied the Pd-catalyzed inter-molecular AAA reaction using our bidentate diphosphonite (BOP) ligands. The BOP ligands exhibit excellent efficacy …