Biology Commons^™

Factors Affecting Adult Foraging And Chick Growth Of Adélie Penguins (Pygoscelis Adeliae) Off The Western Antarctic Peninsula: A Modeling Study, Erik W. Chapman

OES Theses and Dissertations

Coupled individual-based models that simulate Adélie penguin ( Pygoscelis adeliae) chick growth and adult foraging behavior during the chick growth period were developed and used to explore factors that influence chick fledging mass and adult foraging energetics off the western Antarctic Peninsula (WAP). Adélie penguin colonies in this region are undergoing changes in population size that have been correlated with climate-driven alteration of the marine and terrestrial environment. Simulations were selected to highlight possible mechanistic linkages between climate variability and chick growth and adult foraging processes. These processes were the focus of this study because chicks that fledge at …

Thermal Links For The Implementation Of An Optical Refrigerator, John Parker, David Mar, Steven Von Der Porten, John Hankinson, Kevin Byram, Chris Lee, Michael K. Mayeda, Richard C. Haskell, Qimin Yang, Scott R. Greenfield, Richard I. Epstein

All HMC Faculty Publications and Research

Optical refrigeration has been demonstrated by several groups of researchers, but the cooling elements have not been thermally linked to realistic heat loads in ways that achieve the desired temperatures. The ideal thermal link will have minimal surface area, provide complete optical isolation for the load, and possess high thermal conductivity. We have designed thermal links that minimize the absorption of fluoresced photons by the heat load using multiple mirrors and geometric shapes including a hemisphere, a kinked waveguide, and a tapered waveguide. While total link performance is dependent on additional factors, we have observed net transmission of photons with …

Dispersal And Establishment Both Limit Colonization During Primary Succession On A Glacier Foreland, Chad C. Jones, Roger Del Moral

Botany Faculty Publications

Plant colonization can be limited by lack of seeds or by factors that reduce establishment. The role of seed limitation in community assembly is being increasingly recognized, but in early primary succession, establishment failure is still considered more important. We studied the factors limiting colonization on the foreland of Coleman Glacier, Washington, USA to determine the importance of seed and establishment limitation during primary succession. We also evaluated the effects of seed predation, drought and existing vegetation on establishment. We planted seeds of seven species into plots of four different ages and found evidence that both seed and establishment limitation …

An Undescribed Gecko (Gekkonidae: Cyrtodactylus) From Deer Cave, Gunung Mulu National Park, Sarawak, With Comments On The Distribution Of Bornean Cave Geckos, Donald A. Mcfarlane, Joyce Lundberg, Keith Christenson

WM Keck Science Faculty Papers

Geckos of the genus Cyrtodactylus are a speciose group in Southeast Asia, with at least nine species known from the island of Borneo (Das & Ismail, 2001; Das, 2006). Of these species, Cyrtodactylus cavernicolus has the smallest known range and is therefore the most vulnerable, a status that is reflected in the species having been designated a Totally Protected Species in Sarawak. Confirmed records of C. cavernicolus are known only from Niah Cave, located in an isolated limestone block known as the Gunung Subis massif, approximately 13 km² in extent. The Niah Cave Gecko is presumed to be dependent on …

Minimotif Miner 2nd Release: A Database And Web System For Motif Search, Sanguthevar Rajasekaran, Sudha Balla, Patrick R. Gradie, Michael R. Gryk, Krishna Kadaveru, Vamsi Kundeti, Mark W. Maciejewski, Tian Mi, Nicholas Rubino, Jay Vyas, Martin R. Schiller

Life Sciences Faculty Research

Minimotif Miner (MnM) consists of a minimotif database and a web-based application that enables prediction of motif-based functions in user-supplied protein queries. We have revised MnM by expanding the database more than 10-fold to approximately 5000 motifs and standardized the motif function definitions. The web-application user interface has been redeveloped with new features including improved navigation, screencast-driven help, support for alias names and expanded SNP analysis. A sample analysis of prion shows how MnM 2 can be used.

Bats And Bell Holes: The Microclimatic Impact Of Bat Roosting, Using A Case Study From Runaway Bay Caves, Jamaica, Joyce Lundberg, Donald A. Mcfarlane

WM Keck Science Faculty Papers

The microclimatic effect of bats roosting in bell holes (blind vertical cylindrical cavities in cave roofs) in Runaway Bay Caves, Jamaica, was measured and the potential impact of their metabolism on dissolution modelled. Rock temperature measurements showed that bell holes with bats get significantly hotter than those without bats during bat roosting periods (by an average of 1.1 °C). The relationship is clearest for bell holes with more than about 300 g aggregate bat body mass and for bell holes that are moderately wide and deep, of W:D ratio between 0.8 and 1.6. Measurement of temperature decay after abandonment showed …

Prawn Aquaculture In Western Australia. Final Esd Risk Assessment Report For Prawn Aquaculture., Department Of Fisheries Western Australia

Fisheries Management Papers

The Western Australian Department of Fisheries is responsible for the management of aquaculture in WA and is committed to implementing ESD. These principles are contained within the objectives of the Fish Resources Management Act 1994 and the Department is keen to demonstrate both to the Government and the broader community that these principles are being achieved. The Department developed a policy statement in 2002 - Policy for the Implementation of Ecologically Sustainable Development for Fisheries and Aquaculture within Western Australia - (Fletcher 2002) that described its direction to the Department on incorporating ESD within fisheries and aquaculture management.

Using the …

Oxidative Stress, Calcium Homeostasis, And Altered Gene Expression In Human Lung Epithelial Cells Exposed To Zno Nanoparticles, Chuan-Chin Huang

Masters Theses

"The influence of 20 nm ZnO nanoparticles on oxidative stress, intracellular calcium homeostasis, and gene expression was studied in human bronchial epithelial cells (BEAS-2B). ZnO caused a concentration- and time-dependent cytotoxicity while elevating oxidative stress and causing membrane damage (cellular LDH release). There was a remarkably steep relationship between concentration and toxicity at concentrations from 5 to 10 μg/ml. Exposure to ZnO increased intracellular calcium levels in a concentration- and time-dependent manner. Treatment with the antioxidant N-acetylcysteine prevented cell loss and diminished the increase in intracellular calcium concentration, suggesting oxidative stress mediated cytotoxicity. Exposure to a sublethal concentration of ZnO …

Mojave Applied Ecology Notes Winter 2009, Scott R. Abella, Lindsay P. Chiquoine, Alice C. Newton

Mojave Applied Ecology Notes

Chronology of forest structure and use in the Spring Mountains, Soil-Tech’s restoration work balancing construction with nature, species performance and treatment effectiveness for revegetation projects, and strategic research areas for Mojave conservation and management

Charting The Late Cretaceous Seas: Mosasaur Richness And Morphological Diversification, Marcus R. Ross

Faculty Publications and Presentations

Abundant, readily identifiable, and biostratigraphically resolved specimens make mosasaurs ideal candidates to test fluxes in generic richness and morphological trends among marine vertebrates during the late Cretaceous. More than 1800 globally distributed mosasaur specimens are allocated to fifteen substage-level stratigraphically correlated assemblages. These data are quantitatively analyzed to illuminate trends within the group. Following their first appearance in the Cenomanian, mosasaurs experienced a significant radiation in the Coniacian and Santonian. Richness levels continued increasing into the Maastrichtian while mosasaurs incrementally exploited new predatory niches recognized via accumulation of novel dental morphologies. Their extinction at the end of the Cretaceous occurred …

Direct Binding Of Cytosolic Ndp Kinases To Membrane Lipids Is Regulated By Nucleotides, Kimberly A. P. Mitchell, Gabor Szabo, Angela De S . Otero

Faculty Publications and Presentations

In spite of their complete lack of any structural features that characterize membrane proteins, cytosolic nucleoside-diphosphate kinases (NDPKs) have been found repeatedly to associate with membranes. In some instances the recruitment of cytosolic NDPKs to membranes was attributed to interactions with peripheral or integral membrane proteins, but in many cases the mechanism underlying the association of NDPKs with membranes remained unknown. We show here that cytosolic NDPKs bind directly to membrane lipids in a dynamic process that is controlled by its substrates, nucleoside tri- and diphosphates, and can be fully reconstituted with chemically defined, protein-free phospholipids and recombinant NDPK, or …

Methods For The Isolation Of Sensory And Primary Cilia—An Overview, Kimberly A. P. Mitchell, Gabor Szabo, Angela De S. Otero

Faculty Publications and Presentations

Detailed proteomic analyses of mammalian olfactory and rod photoreceptor sensory cilia are now available, providing an inventory of resident ciliary proteins and laying the foundation for future studies of developmental and spatio-temporal changes in the composition of sensory cilia. Cilia purification methods that were elaborated and perfected over several decades were essential for these advances. In contrast, the proteome of primary cilia is yet to be established, because purification procedures for this organelle have been developed only recently. In this chapter we review current techniques for the purification of olfactory and photoreceptor cilia, and evaluate methods designed for the selective …

The Malina Oceanographic Expedition: How Do Changes In Ice Cover, Permafrost And Uv Radiation Impact On Biodiversity And Biogeochemical Fluxes In The Arctic Ocean?, Phillippe Massicotte, Rainer Amon, David Antoine, Philippe Archambault, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Malik, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Et. Al.

Faculty Publications

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables was measured across seven shelf–basin transects (south-north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll-a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a barge …

Nona-Arginine Peptides Facilitate Cellular Entry Of Semiconductor Nanocrystals: Mechanisms Of Uptake, Yi Xu

Masters Theses

"Luminescent semiconductor quantum dots (QDs) have recently been used for delivering and monitoring biomolecules, such as drugs and proteins. However, QDs alone have a very low efficiency of transport across the plasma membrane. In order to increase the efficiency of QD delivery, synthetic nona-arginine (sR9) was used, a cell penetrating peptide, to facilitate uptake. Data demonstrated that sR9 could significantly increase the cellular uptake of QDs by noncovalent binding between QDs and sR9. Furthermore, the mechanisms of QD/sR9 cellular internalization were investigated. Low temperature and metabolic inhibitors markedly inhibited the uptake of QD/sR9, indicating that internalization is an energy-dependent process. …

Electricity Generation And Ethanol Production Using Iron-Reducing, Haloalkaliphilic Bacteria, Varun Paul

Masters Theses

"Microbial life in extreme environments has been studied primarily for their metabolic activities. Very few commercial or industrial applications have been known from these systems. In this study, the metabolic pathways and properties of bacteria from a haloalkaliphilic environment of Soap Lake, Washington were employed in two research applications related to energy production. In the first study, the bacterial cultures that were known to reduce iron (III) were used in a Microbial Fuel Cell (MFC) reactor. Iron reducing bacteria have shown to shunt their electrons on to the surface of a carbon electrode of an MFC, and the electrons can …

Synthesis Of Fatty Acid Binding Protein Inhibitors: A New Approach For Diabetes Treatment, Shekelia Baccus, M. Perry Davis Jr, David R. Magnin

Journal of the South Carolina Academy of Science

No abstract provided.

Generation Of A Retroviral Vector That Expresses An Anti-Hiv-1 Tat Hammerhead Ribozyme, Lindsey E. Padgett, William H. Jackson

Journal of the South Carolina Academy of Science

No abstract provided.

Effect Of Thaw Temperature On Murine Blastocyst Development, Heather M. Barton, H. Lee Higdon Iii, Ph.D., Jennifer E. Graves-Herring M.S., William R. Boone, Ph.D.

Journal of the South Carolina Academy of Science

No abstract provided.

The Effects Of Growing Method And The Food Processing System On Bacterial Concentration In Spinach, Thad S. Moore, Lisa W. Norman

Journal of the South Carolina Academy of Science

No abstract provided.

Biology In Mathematics At The University Of Richmond, Lester Caudill

Department of Math & Statistics Faculty Publications

In an effort to meet the needs of science students for modeling skills, three new courses have been created at the University of Richmond: Scientific Calculus I and II, and Mathematical Models in Biology and Medicine. The courses are described, and lessons learned and future directions are discussed.

Management And Social Indicators Of Soil Carbon Storage In A Residential Ecosystem, Midlothian, Va, Christopher M. Gough, Eliza A. Fritz

Virginia Journal of Science

Soil carbon storage- defined here as carbon mass per unit ground area- is an important ecosystem service, sequestering carbon that might otherwise exist in atmospheric CO₂ . Significant attention has focused on the effects that humans have on carbon cycling, but little is known about how human behaviors and attitudes relate to lawn carbon storage. The objectives of this study were to conduct household surveys in concert with soil carbon sampling in a 10-year-old exurban neighborhood near Richmond, Virginia to quantify differences in soil carbon storage between residential lawns and mixed pine-hardwood forest fragments, and to determine how lawn …

Protein-Protein Docking Using Region-Based 3d Zernike Descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur.

Results

We present a novel protein docking algorithm based …

Application Of 3d Zernike Descriptors To Shape-Based Ligand Similarity Searching, Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed.

Results

In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, …

The Epidemiological Status Of Pav1, And The Effects Of Infection On Caribbean Spiny Lobster (Panulirus Argus) Condition, Olfaction, And Predation Risk, Donald C. Behringer, Mark J. Butler Iv, Jeffrey D. Shields

Biological Sciences Faculty Publications

No abstract provided.

The Influence Of Fallback Foods On Great Ape Tooth Enamel, Paul J. Constantino, Peter W. Lucas, James J.-W. Lee, Brian R. Lawn

Biological Sciences Faculty Research

Lucas and colleagues recently proposed a model based on fracture and deformation concepts to describe how mammalian tooth enamel may be adapted to the mechanical demands of diet (Lucas et al.: Bioessays 30[2008] 374-385). Here we review the applicability of that model by examining existing data on the food mechanical properties and enamel morphology of great apes (Pan, Pongo, and Gorilla). Particular attention is paid to whether the consumption of fallback foods is likely to play a key role in influencing great ape enamel morphology. Our results suggest that this is indeed the case. We also consider the implications of …

In Vitro Evaluation Of Bioactive Glass Scaffolds And Modified Bioactive Glasses With An Osteogenic Cell Line, Vernon C. Modglin

Masters Theses

"This investigation consisted of two parts focused on bioactive glasses and scaffolds for in vitro growth of bone cells for tissue engineering and bone repair. The first part involved evaluation of the ability of two new types of porous 13-93 bioactive glass scaffolds to support the growth and differentiation of mouse MLO-AS cells, an established osteogenic cell line used as a model of developing bone tissue. The two scaffold types tested included 13-93 glass fiber and trabecular-like scaffolds seeded with MLO-AS cells and cultured for intervals of 2 to 12 days. Collectively, in vitro results indicate that the 13-93 glass …

Faculty Should Consider Peer Review As A Means Of Improving Students' Scientific Reasoning Skills, Briana Timmerman, Denise Strickland

Journal of the South Carolina Academy of Science

No abstract provided.

The Integrated Biomedical Science Graduate Program At The University Of South Carolina, Richard Hunt

Journal of the South Carolina Academy of Science

No abstract provided.

The Effect Of Incubation Time On The Generation Of Benzene In Sierra Mist Free, Sarah Law

Journal of the South Carolina Academy of Science

No abstract provided.

Downregulation Of Hiv-1 Vif By A Hammerhead Ribozyme Expressed From A Retroviral Vector, Audrey M. Hendley, William Jackson

Journal of the South Carolina Academy of Science

No abstract provided.