Biology Commons^™

Temperature Changes Resulting From A Gaalas Laser In The Decontamination Of A Failing Dental Implant, Adam B. Oppenheimer

Journal of the South Carolina Academy of Science

No abstract provided.

Where Do Mouse Embryos Thrive Best? Comparison Of Mammalian Embryo Development Under Varying Laboratory Environments, Yvonne K. Kao, 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.

Potential Export Of Unattached Benthic Macroalgae To The Deep Sea Through Wind Driven Langmuir Circulation, H. M. Dierssen, Richard C. Zimmerman, Lisa A. Drake, David J. Burdige

OES Faculty Publications

Carbon export to the deep sea is conventionally attributed to the sinking of open ocean phytoplankton. Here, we report a Langmuir supercell event driven by high winds across the shallow Great Bahama Bank that organized benthic non-attached macroalgae, Colpomenia sp., into visible windrows on the seafloor. Ocean color satellite imagery obtained before and after the windrows revealed a 588 km² patch that rapidly shifted from highly productive macroalgae to bare sand. We assess a number of possible fates for this macroalgae and contend that this event potentially transported negatively buoyant macroalgae to the deep Tongue of the Ocean …

Geobiology: Evidence For Early Life On Earth And The Search For Life On Other Planets, Sherry L. Cady, Nora Noffke

OES Faculty Publications

Extensive research efforts in the subdisciplinary field of geobiology have focused on the interactions between Earth and life through time. As a consequence, gaps in our knowledge of Earth’s history are closing, and the search for life beyond Earth is expanding. A few examples of geobiology studies designed to advance our understanding of life on early Earth and to improve the chances of finding life on other planets are provided to highlight recent developments and research areas that are on the verge of new discoveries.

Synergistic Effects Of Iron And Temperature On Antarctic Phytoplankton And Microzooplankton Assemblages, J. M. Rose, Y. Feng, G. R. Ditullio, R. B. Dunbar, C. E. Hare, P. A. Lee, M. Lohan, M. Long, W. O. Smith Jr., B. Sohst, S. Tozzi, Y. Zhang, D. A. Hutchins

OES Faculty Publications

Iron availability and temperature are important limiting factors for the biota in many areas of the world ocean, and both have been predicted to change in future climate scenarios. However, the impacts of combined changes in these two key factors on microbial trophic dynamics and nutrient cycling are unknown. We examined the relative effects of iron addition (+1 nM) and increased temperature (+4° C) on plankton assemblages of the Ross Sea, Antarctica, a region characterized by annual algal blooms and an active microbial community. Increased iron and temperature individually had consistently significant but relatively minor positive effects on total phytoplankton …

Effects Of Olfactory And Visual Predators On Nest Success And Nest-Site Selection Of Waterfowl In North Dakota, Jennifer Borgo

Green Canyon Environmental Research Area, Logan Utah

No abstract provided.

Occurrence Of Digenean Larvae In Freshwater Snails In The Ruvu Basin, Tanzania, G. Nkwengulila, E. S. P. Kigadye

Tanzania Journal of Science

A survey was carried out on digenean larvae infecting freshwater snails in five habitats in Dar es Salaam, Ruvu and Morogoro. 9424 snails belonging to 12 species from five families were examined for digenean infection from July 1996 – June 1997. 20 morphologically distinguishable cercariae were recovered. Multiple infections were not recorded. While the general prevalence of digeneans in snails was low (3.5%), variations occurred between seasons, among habitats and snail host species. Prevalence was high during the dry season but low in the rain season. Among habitats, highest prevalence was recorded at Kinondoni pond and lowest at Ruvu ponds, …

Fisheries Occasional Publication No.72 - Western Rock Lobster Ecological Effects Of Fishing Research Plan., Rhys Brown

Fisheries Occasional Publications

The commercial West Coast Rock Lobster Fishery (WCRLF) targets the western rock lobster (WRL), Panulirus cygnus, averaging approximately 10,000 tonnes of lobsters each year. Currently approximately 450 to 500 boats operate in the Fishery in waters ranging from 5 m to 200 m depth adjacent to the Western Australian coast and stretching from Cape Leeuwin in the south to Shark Bay in the north. The Fishery is managed by the Department of Fisheries (DoF) in Western Australia, using an input control system designed to constrain exploitation/fishing effort and deliver sustainable catches. The annual value of the catch is estimated at …

Seasonal Changes In A Eutrophic Lake, Wilgreen Lake, Madison County, Kentucky, Richard D. Stockwell, Walter S. Borowski

EKU Faculty and Staff Scholarship

WilgreenLake (Madison County, Kentucky) covers ~169 acres, formed in 1966 by damming Taylor Fork. The Wilgreen watershed drains residential developments, modified woodlands, cattle pasture, and some industrial/urban areas in the city of Richmond. The lake is deemed “nutrient impaired” by the EPA.

Our main objective is to document the seasonal changes in key lake parameters from summer stratification through fall overturn over 4 months of sampling, August through November, 2008. We collect temperature, oxygen, pH, and conductivity data from 19 stations at depth intervals of 1 meter using an YSI multi-probe. Concurrent with collecting these framework data, we take water …

Comparisons Of Lake Characteristics With The Fish Species Present, John Carrier

Honors Capstones

Capstone submitted as a graduate requirement for the BSU Honors Program.

Mojave Applied Ecology Notes Fall 2008, Alice Miller, Joshua Hoines, Scott R. Abella

Mojave Applied Ecology Notes

Effects of wildfires in Joshua Tree National Park, Blackbrush masting volunteer seed collection effort, new book chapter on Mojave revegetation, Natural Areas Association presentations.

Corallivorous Reef Fishes As Potential Vectors Of Coral Disease Based On A Study Of Dietary Preferences, Tanya Rogers

Independent Study Project (ISP) Collection

The prevalence of coral disease appears to be increasing worldwide, although little is known about how these diseases are transmitted between coral colonies. To examine whether corallivorous fishes could potentially act as disease vectors, this study examined whether and which fish species feed on diseased coral, and whether these fishes actively target diseased coral sections. Branches of Acropora muricata with brown band disease were filmed in the field, and bites taken by fishes on different sections of the coral (live tissue, tissue margin, disease band, dead skeleton, and algae) were recorded. For each fish species, electivity indices were calculated for …

Unraveling Protein Networks With Power Graph Analysis, Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder

Faculty Publications, Computer Science

Networks play a crucial role in computational biology, yet their analysis and representation is still an open problem. Power Graph Analysis is a lossless transformation of biological networks into a compact, less redundant representation, exploiting the abundance of cliques and bicliques as elementary topological motifs. We demonstrate with five examples the advantages of Power Graph Analysis. Investigating protein-protein interaction networks, we show how the catalytic subunits of the casein kinase II complex are distinguishable from the regulatory subunits, how interaction profiles and sequence phylogeny of SH3 domains correlate, and how false positive interactions among high-throughput interactions are spotted. Additionally, we …

Mojave Applied Ecology Notes Summer 2008, Doug Merkler, Scott R. Abella, Dianne N. Bangle, Donovan J. Craig, Jessica E. Spencer, Alex Suazo

Mojave Applied Ecology Notes

Soil climate project, rare plant monitoring, JFS update, granivory and Sahara mustard

A Strategy For Managing The Recreational Catch Of Demersal Scalefish In The West Coast Bioregion. Decisions By The Minister For Fisheries, Jon Ford (Minister For Fisheries; The Kimberley, Pilbara And Gascoyne)

Fisheries Management Papers

The following recreational fisheries management package is a result of an extensive public consultation process. The package has been carefully developed to deliver the required reduction in catches. It is important to understand that each management measure contributes to the reduction in catches necessary to give these stocks a chance to rebuild and that no measure on its own will deliver the required reduction in catch.

To ensure the ongoing recovery of stocks, an adaptive approach to management has been adopted. This approach will involve an ongoing review of the effectiveness of these management arrangements, and take into account the …

Neural Network Models For Solving The Maximum Flow Problem, S. Effati, M. Ranjbar

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, two new neural network models for solving the maximum flow problem are presented. The maximum flow problem in networks is formulated as a special type of linear programming problem and it is solved by appropriately defined neural networks. The nonlinear neural networks are able to generate optimal solution for maximum flow problem. We solve neural network models by one of the numerical method. Finally, some numerical examples are provided for the sake of illustration.

Improving The Computer Science In Bioinformatics Through Open Source Pedagogy, John David N. Dionisio, Kam D. Dahlquist

Biology Faculty Works

Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total "incubation time" of six months.

An Improved String Composition Method For Sequence Comparison, Guoquing Lu, Shunpu Zhang, Xiang Fang

Biology Faculty Publications

Background: Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational limitations. Consequently, alignment-free methods have been explored as important alternatives in estimating sequence similarity. Of the alignment-free methods, the string composition vector (CV) methods, which use the frequencies of nucleotide or amino acid strings to represent sequence information, show promising results in genome sequence comparison of prokaryotes. The existing CV-based methods, however, suffer certain statistical problems, thereby underestimating the amount of evolutionary …

Population Dynamics Of Freshwater Invertebrates In Beltrami County, Amanda Johnson

Honors Capstones

Capstone submitted as a graduate requirement for the BSU Honors Program.

The Shapley Value Of Phylogenetic Trees, Claus-Jochen Haake, Akemi Kashiwada '05, Francis E. Su

All HMC Faculty Publications and Research

Every weighted tree corresponds naturally to a cooperative game that we call a tree game; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space …

Mojave Applied Ecology Notes Spring 2008, Lesley Defalco, E. Cayenne Engel, Scott R. Abella, Jessica E. Spencer, Jill E. Craig

Mojave Applied Ecology Notes

Post-fire restoration, fire chronosequence study, Joint Fire Science update, Weed Sentry program and DNWR surveys

Volume 01, Jessica Fields, Stephanie Neeley, Derek W. Hambright, Mary E. Lehman, Andrew R. Grzankowski, Zachary Johnson, Boone M. Prentice, Ashley M. Swandby, Victoria Morgan, Katie Williamson, Kristine G. Bender, Katelyn N. Romaine, D. Nicole Swann, Jessica Fox, Mike Mcateer, Alex Grabiec, Laura Nodtvedt, Nick Costa, Rachel Wolfe, Zack Dalton

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Three Decades of Digging: Undergraduate Archeology at Longwood by Jessica Fields and Stephanie Neeley

Interactions of Allelopathy and Heat Stress in Plants by Derek W. Hambright and Mary E. Lehman

Inertial Electrostatic Confinement D-D Fusion Device: Construction and Simulation by Andrew R. Grzankowski

Shackled Nim by Zachary Johnson

Development of GC-MS and Chemometric Methods for the Analysis of Accelerants in Arson Cases by Boone M. Prentice

A Comparison of Image Analysis Methods in cDNA Microarrays by Ashley M. Swandby

Perceived Sexual Activity of Short and Long-Term Relationships by Victoria Morgan and Katie Williamson

Elderly …

A Watershed Analysis Of Pattee Pond: Implications For Water Quality And Land Use Management, Problems In Environmental Science Course (Biology 493), Colby College, Colby Environmental Assessment Team, Colby College

Colby College Watershed Study: Pattee Pond (2008, 1992)

The Colby Environmental Assessment Team (CEAT) investigated the impact of land use patterns on the water quality of Pattee Pond in Winslow, Maine, during the summer and fall of 2008. Physical, chemical, and biological characteristics of water quality were analyzed to evaluate the current health of the lake. Data collected were compared with previous studies conducted by the Maine Department of Environmental Protection (DEP) and CEAT to examine changes in water quality and land use over time. Trends in Pattee Pond water quality suggest an improvement since the 1970s. However, the lake is still experiencing algal blooms resulting from phosphorus …

Sustainability In A Time Of Climate Change: Developing An Intensive Research Framework For The Platte River Basin And The High Plains Proceedings From The 2008 Climate Change Workshop, Monica Norby, Ashley Washburn

Office of Research and Economic Development: Publications

Proceedings from the 2008 Climate change Workshop, Nebraska Sandhills, May 19-22, 2008. Hosted by the University of Nebraska–Lincoln and the U.S. Geological Survey

The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs

Biology Department Faculty Works

BackgroundThe bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion.ResultsPhylogenetic concordance between …

Open Circuit Potential Shifts Of Activated Carbon In Aqueous Solutions During Chemical And Adsorption Interactions, Mikhail M. Goldin, Vladimir A. Kolesnikov, Mogely Sh. Khubutiya, Alexander G. Volkov, Gary J. Blanchard, Anatoly K. Evseev, Mark M. Goldin

Faculty Publications and Presentations

Interaction of certain inorganic and organic compounds with activated carbon and the effect of such interaction on open circuit potential of activated carbon were studied. Open circuit potential shifts were observed for an overwhelming majority of the substances and brands of activated carbons investigated. Both negative and positive potential shifts were observed. It was shown that open circuit potential shifts for organic substances depend on degree of coverage of the activated carbon surface. Whereas adsorption of investigated organic compound on activated carbon led to positive potential shifts, desorption of adsorbates from the activated carbon surface led to potential shifts in …

Mutational Analysis Of The Stability Of The H2a And H2b Histone Monomers, Matthew R. Stump, Lisa M. Gloss

Faculty Publications - Department of Biological & Molecular Science

The eukaryotic histone heterodimer H2A–H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The …

Mojave Applied Ecology Notes Winter 2008, Scott R. Abella, E. Cayenne Engel, Jill E. Craig

Mojave Applied Ecology Notes

Mojave Desert collaborative projects, fire history in Spring Mountains, Northshore Road rehabilitation, wildfires and invasive plants in American deserts conference, weed sentry surveys

The Identification And Characterization Of Phenylalanine Ammonia-Lyase Gene Family Members In Glycine Max, Erin Kathleen Pringle

Masters Theses

"Gene families are collections of genes with similar functions. Studying gene families is important for understanding the evolution of genes and manipulating genes. Phenylalanine ammonia-lyase (PAL) is an enzyme found in plants. It catalyzes the deamination of phenylalanine to produce cinnamic acid. Genes for PAL have been identified in many different plant species. This project used the known sequence for the PAL1 gene in Glycine max to find other PAL genes in Glycine max"--Abstract, page iii.

Role Of Microtubules In Budding Yeast Cytokinesis, Su Young Park

Masters Theses

"Cytokinesis is an important step to finish cell cycle events and separate into two daughter cells. This event is driven by actomyosin ring contraction. In budding yeast, the mitotic exit network (MEN) controls completion of ana/telophase by signaling events. Bub2 is a mitotic exit network regulator and binds to Tem1p which is an important component in MEN. Mad2 is a component of a separate spindle checkpoint. Mad2 dependent pathway prevents the metaphase to anaphase transition under spindle damage. Because yeast cells have cell walls, septum formation follows actin ring contraction. Here it was investigated how microtubule defects affect cytokinesis in …