Digital Commons Network^™

Clustering Neural Spike Trains With Transient Responses, John D. Hunter, Jianhong Wu, John Milton

WM Keck Science Faculty Papers

The detection of transient responses, i.e. nonstationarities, that arise in a varying and small fraction of the total number of neural spike trains recorded from chronically implanted multielectrode grids becomes increasingly difficult as the number of electrodes grows. This paper presents a novel application of an unsupervised neural network for clustering neural spike trains with transient responses. This network is constructed by incorporating projective clustering into an adaptive resonance type neural network (ART) architecture resulting in a PART neural network. Since comparisons are made between inputs and learned patterns using only a subset of the total number of available dimensions, …

The Impact Of Repeated Rounds Of Mass Drug Administration With Diethylcarbamazine Plus Albendazole On Bancroftian Filariasis In Papua New Guinea, Gary J. Weil, Will Kastens, Melinda Susapu, Sandra J. Laney, Steven A. Williams, Christopher L. King, James W. Kazura, Moses J. Bockarie

Biological Sciences: Faculty Publications

Background: This study employed various monitoring methods to assess the impact of repeated rounds of mass drug administration (MDA) on bancroftian filariasis in Papua New Guinea, which has the largest filariasis problem in the Pacific region.

Methodology/Principal Findings: Residents of rural villages near Madang were studied prior to and one year after each of three rounds of MDA with diethylcarbamazine plus albendazole administered per World Health Organization (WHO) guidelines. The mean MDA compliance rate was 72.9%. Three rounds of MDA decreased microfilaremia rates (Mf, 1 ml night blood by filter) from 18.6% pre-MDA to 1.3% after the third MDA (a …

Production Of Marine Trematode Cercariae: A Potentially Overlooked Path Of Energy Flow In Benthic Systems, David W. Thieltges, Xavier De Montaudouin, Brian L. Fredensborg, K. Thomas Jensen, Janet Koprivnikar, Robert Poulin

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Parasites, in particular trematodes, are unseen but ubiquitous components of marine intertidal ecosystems. Although parasites are known to affect population dynamics and food web structure, their potential function as an unrecognized path of energy flow in these ecosystems is yet to be quantified. We use published data on rates at which trematodes produce free-swimming infective larvae (cercariae) that are released from their gastropod intermediate hosts to investigate patterns in cercarial output as a function of different variables, and to calculate the annual production of cercariae in different marine benthic systems. Across 18 trematode species, cercarial output (no. cercariae shed snail–1 …

Does Shape Predict Performance? An Analysis Of Morphology And Swimming Performance In Great Basin Fishes, John R. Aedo

Theses and Dissertations

Swimming performance strongly influences fitness in aquatic organisms and is closely tied to external body morphology. Although this connection has been closely examined at the individual and species level, few studies have focused on this relationship as it pertains to functional group assemblages. Using functional groups based on similarities in habitat use and morphology, I tested the hypothesis that swimming performance can be reliably predicted by functional group composition. I measured swimming performance as burst speed using a simulated predator attack and as prolonged speed using a step-endurance test in a laboratory flume. I measured morphology using geometric morphometric techniques. …

Trichomycetes From Lentic And Lotic Aquatic Habitats In Ontario, Canada, D. B. Strongman, Merlin M. White

Biology Faculty Publications and Presentations

Fungi and protists make up an ecological group, trichomycetes, that inhabit the guts of invertebrates, mostly aquatic insects. Trichomycetes are reported herein from arthropods collected in lotic habitats (fast flowing streams) and lentic environments (ponds, ditches, seeps, and lakes) from 11 sites in Algonquin Park and 6 other sites in Ontario, Canada. Thirty-two trichomycete species were recovered, including 7 new species: Legeriomyces algonquinensis, Legeriosimilis leptocerci, Legeriosimilis whitneyi and Paramoebidium umbonatum are described from mayfly nymphs (Ephemeroptera); Pennella digitata and Glotzia incilis from black fly and midge larvae (Diptera), respectively; and Arundinula opeongoensis from a crayfish (Crustacea). Legeriomyces rarus Lichtw. & …

Does Light Control Algal Abundance In Large River Systems?, Amy Macdonald

Theses and Dissertations

A limited amount of research has been done to investigate the factors influencing algal abundance in large river systems. This study examines light as the primary factor that controls algal abundance in the Upper Mississippi, Missouri and Ohio Rivers. Data were collected for 2004 in conjunction with the Environmental Monitoring Assessment Program- Great River Ecosystems EMAP-GRE project using EPA approved methods. Chlorophyll a concentrations were 34.6 µg•L-1 in the Upper Mississippi, 19.8 µg•L-1 in Missouri River and 9 µg•L-1 in the Ohio River for 2004. Chlorophyll a concentrations were significantly different among the three rivers (p<0.0001) but not between years. Inter-river variation could be loosely correlated with light availability: mean Average Irradiance Dosages, which consider factors that affect light climate (depth, transparency, velocity, surface irradiance), by river corresponded with mean chlorophyll a levels by river. Intra-river variation seemed to be due to both the influence of light and nutrients.

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.

The Biological Soil Crusts Of The San Nicolas Island: Enigmatic Algae From A Geographically Isolated Ecosystem, Valerie R. Flechtner, Jeffrey R. Johansen, Jayne Belnap

Biology

Composite soil samples front 7 sites on San Nieolas Island were evaluated quantitatively and qualitatively for the presence of cyanobacteria and enkaryotic microalgae. Combined data demonstrated a rich algal flora with 19 cyanobacterial and 19 eukaryotic microalgal genera being identified, for a total of 56 species. Nine new species were identified and described among the cyanobacteria and the enkaryotic microalgae that were isolated: Leibleinia edaphica, Aphanothece maritima, Chroococcidiopsis edaphica, Cyanosarcina atroceneta, Hassallia californica, Hassallia pseudo-ramosissima, Microchaete terrestre, Palmellopsis californicus, and Pseudotetracystis compactis. Distinct distributional patterns of algal taxa existed among sites on the island and among soil algal floras of …

Yellow Head Virus: Transmission And Genome Analyses, Hongwei Ma

Dissertations

Yellow head virus (YHV) is an important pathogen to shrimp aquaculture. Among 13 species of naturally YHV-negative crustaceans in the Mississippi coastal area, the daggerblade grass shrimp, Palaemonetes pugio, and the blue crab, Callinectes sapidus, were tested for potential reservoir and carrier hosts of YHV using PCR and real time PCR. The YHV replicated in the daggerblade grass shrimp, and was still detectable on 36 d post-inoculation, causing 8% mortality after injection. However, YHV did not replicate in the blue crab. These data suggest that the daggerblade grass shrimp could act as a reservoir host for YHV. Storage conditions of …

Biological Responses In A Dynamic Bouyant River Plume, Mark A. Moline, Thomas K. Frazer, Robert Chant, Scott Glenn, Charles A. Jacoby, John R. Reinfelder, Jennifer Yost, Meng Zhou, Oscar Schofield

Biological Sciences

Buoyant river plumes are highly dynamic and often characterized by marked physical and chemical gradients that interact to drive biological responses. For example, interactions among factors resulting in algal growth (e.g., nutrient and light availability) and algal loss (e.g., sinking and zooplankton grazing) vary with spatiotemporal changes in physics and chemistry. The nature of these interactions profoundly influences the transfer and transformation of materials carried by the plume, including nutrients and metals. In April 2005, during the Lagrangian Transport and Transformation Experiment (LaTTE), water from the Hudson River recirculated in a nearshore eddy before moving southward to mix with relatively …

An Analysis Of Illegal Bushmeat Availability In Local Restaurants Located In Voi, Kenya, Bridget A. Sutton

Masters Theses & Specialist Projects

The illegal bushmeat harvest has been identified as a reason for declining wildlife populations throughout much of Africa. For many years the trade was thought to exist primarily in Western Africa. The illegal use of bushmeat in Eastern Africa, including Kenya, went undocumented and unstudied. In 2004, the Born Free Foundation published a study which claimed illegal sale of wild game was substantial in butcheries throughout Nairobi, Kenya. In an effort to determine other markets of the commercial trade, the goal of this study was to analyze local restaurants in Voi, Kenya for illegal bushmeat sale. The town of Voi …

Recombination-Based In Vivo Expression Technology Identifies Helicobacter Pylori Genes Important For Host Colonization, Andrea Castillo, Andrew J. Woodruff, Lynn E. Connolly, William E. Sause, Karen M. Ottemann

Biology Faculty Publications

Here we undertook to identify colonization and gastric disease-promoting factors of the human gastric pathogen Helicobacter pylori as genes that were induced in response to the stomach environment. Using recombination-based in vivo expression technology (RIVET), we identified six promoters induced in the host compared to laboratory conditions. Three of these promoters, designated Pivi10, Pivi66, and Pivi77, regulate genes that H. pylori may use to interact with other microbes or the host. Pivi10 likely regulates the mobA, mobB, and mobD genes, which have potential roles in horizontal gene transfer through plasmid mobilization. Pivi66 occurs in the cytotoxin-associated gene pathogenicity island, a …

Dispersal Of The Hudson River Plume In The New York Bight: Synthesis Of Observational And Numerical Studies During Latte, Robert J. Chant, John Wilkin, Weifeng Zhang, Byoung-Ju Choi, Eli Hunter, Renato Castelao, Scott Glenn, Joe Jurisa, Oscar Schofield, Robert Houghton, Josh Kohut, Thomas K. Frazer, Mark A. Moline

Biological Sciences

Observations and modeling during the Lagrangian Transport and Transformation Experiment (LaTTE) characterized the variability of the Hudson River discharge and identified several freshwater transport pathways that lead to cross-shelf mixing of the Hudson plume. The plume’s variability is comprised of several different outflow configurations that are related to wind forcing, river discharge, and shelf circulation. The modes are characterized by coastal current formation and unsteady bulge recirculation. Coastal currents are favored during low-discharge conditions and downwelling winds, and represent a rapid downshelf transport pathway. Bulge formation is favored during high-discharge conditions and upwelling winds. The bulge is characterized by clockwise …

Dietary Exposure To 2,2´,4,4´-Tetrabromodiphenyl Ether (Pbde-47) Alters Thyroid Status And Thyroid Hormone–Regulated Gene Transcription In The Pituitary And Brain, Sean C. Lema, Jon T. Dickey, Irvin R. Schultz, Penny Swanson

Biological Sciences

No abstract provided.

Integrating Development And Evolution In Psychology: Looking Back, Moving Forward, David S. Moore

Pitzer Faculty Publications and Research

This work is the editorial for a special edition of New Ideas in Psychology titled Integrating Development and Evolution in Psychology.

Distribution Patterns Of Sciurus Niger (Eastern Fox Squirrel) Leaf Nests Within Woodlots Across A Suburban/Urban Landscape, Carmen M. Salsbury

Scholarship and Professional Work - LAS

To determine habitat characteristics that influence Sciurus niger (Eastern Fox Squirrel) abundance and distribution within a suburban/urban landscape in the midwestern United States, I documented the density and placement of fox squirrel leaf nests in 20 woodlots in the Indianapolis metropolitan area, Marion County, IN. The woodlots varied in size (0.94 to 19.5 ha), approximate age, shape, and degree of isolation from other woodlots and suitable squirrel habitat in the surrounding area. Only 8.0% of nests were located in a tree with another nest, and nests were randomly distributed in all but one woodlot, where they were uniformly dispersed. Nest …

Preliminary Analysis Of The Ecology And Geography Of The Asian Nuthatches (Aves: Sittidae), Shaily Menon, Zafar-Ul Islam, Jorge Soberon, A. Townsend Peterson

Peer Reviewed Publications

We explored distributions of Asian nuthatch species in ecological and geographic space using ecological niche modeling based on occurrence data associated with specimens and observations. Nuthatches represent a well-defined clade occurring throughout the Northern Hemisphere, but are most diverse in southern Asia where 15 of the 24 species occur and where the lineage is believed to have evolved. Species richness was focused in a narrow east-west band corresponding to the forested parts of the Himalayas with a maximum number of nine species predicted present in these foci. The distributional predictions have a mid-elevation focus with highest species diversity between 1,000 …

The Ecological Importance Of Severe Wildfires: Some Like It Hot, Richard L. Hutto

Biological Sciences Faculty Publications

Many scientists and forest land managers concur that past fire suppression, grazing, and timber harvesting practices have created unnatural and unhealthy conditions in the dry, ponderosa pine forests of the western United States. Specifically, such forests are said to carry higher fuel loads and experience fires that are more severe than those that occurred historically. It remains unclear, however, how far these generalizations can be extrapolated in time and space, and how well they apply to the more mesic ponderosa pine systems and to other forest systems within the western United States. I use data on the pattern of distribution …

"Absolutely Part Of What We Should Be Doing": Kevin Curry, Water Filters And The International Mission Of The Modern University, Andrew C. Holman

Bridgewater Review

No abstract provided.

Construction Of A New Model System In Saccharomyces Cerevisa To Study Yopo And Identify Its Targets, Laura Nejedlik

Dissertations

Yersinia species use a type three secretion system (TTSS) to inject Yersinia outer proteins (Yops) into the target cell. The effector YopO is a serine/threonine kinase which upon association with actin becomes active. However, activation of the kinase is not required for actin disruption. YopO also contains a Rho/Rac binding domain, but it is unclear how it affects these proteins.

We have established an expression system in Saccharomyces cerevisiae to study YopO. The expression vector contains a GAL1 promoter for inducible expression of YopO as well as a V5 epitope used for visualization of each Yop. We have shown that …

Monogenic Control Of Sex-Limited Colouration In The Honey Gourami, Trichogaster Chuna, Jack Frankel

Department of Biology Faculty Publications

Of the numerous subtropical and tropical freshwater speciesof  fish,  labyrinth  fish  are  among  the  most  varied  in  bodymarkings and colouration patterns. Four taxonomic families(Belontiidae, Anabantidae, Helostomatidae, and Osphrone-midae)  of  the  suborder  Anabantoidei  comprise  the  ‘tradi-tional’  labyrinth  fishes,  a  group  of  about  80  African  andSoutheast Asian species (Linke 1991).  These Anabantoidsare popular with aquarists due to their interesting reproduc-tive behaviours, with males of most species brooding eggs intheir mouths or in floating bubble nests (Vevers 1980; Linke1991; Axelrod and Vorderwinkler 1995; Mills 2000).  Theyhave also been the focus of genetic, environmental, and mor-phological studies (Sommer 1982; Gosline 1985; Klinkhardtet  al.  1995; …

Characterization Of The Ap-1 And Nf-Kappa B Transcription Factors In The U-87 Mg Astrocytoma Cell Line, Denise L. Smith

Dissertations

Growth factors, signaling molecules and transcription factors are frequently mutated in cancer and platelet-derived growth factor (PDGF) has been shown to be over-expressed in most gliomas. In the astrocytoma cell line U-87 MG, the over-expression of PDGF has been shown to lead to over-expression of transcription factors activator-protein-1 (AP-1) and nuclear factor-kappa B (NF-κB), and it is believed that the individual subunits of AP-1 (c-Jun, JunB, JunD, c-Fos, FosB, Fra-1, and Fra-2) and NF-κB (c-Rel, p50, p52, p65, and RelB) play different roles in proliferation, survival and differentiation in the U-87 MG cell line.

To assess these different roles, transient …

Adverse Effects Of Chronic Circadian Desynchronization In Animals In A "Challenging" Environment, Fabian Preuss, Tueming Tang, Aaron D. Laposky, Deanna M. Arble, Ali Keshavarzian, Fred W. Turek

Biological Sciences Faculty Research and Publications

Continuous disruption of circadian rhythms, as seen in human shift workers, has been associated with the development of a number of adverse mental and physiological conditions. However, scientific evidence linking circadian disruption to overall health, particularly in animal models, is not well documented. In this study, we have demonstrated that exposing C57BL/6J mice to 12-h phase shifts every 5 days for 3 mo had no effect on body weight or intestinal physiology. However, when animals were further challenged with dextran sodium sulfate to induce colitis, chronic shifting of the light-dark cycle led to a dramatic increase in the progression of …

A Cell Biology Laboratory Exercise To Study Sub-Cellular Organelles In Drosophila, Meghana Tare, Amit Singh

Biology Faculty Publications

The fast-changing scenario of undergraduate education puts emphasis on introducing students to hands-on techniques as part of their laboratory courses. In order to cater to large numbers of students and the time constraints involved with undergraduate level laboratory courses, there is a need for development of experiments that are cost effective and can be completed in a defined time frame. We have devised a laboratory exercise for teaching cell biology using the Drosophila melanogaster model. Drosophila can be reared in a short period of time in a cost effective manner. We used Drosophila tissue to study the sub-cellular organization of …

Evaluation Of Methods For Establishing Vegetation In Created Wetland Mitigation Sites In Eastern Nebraska, Andrew A. Miller

Student Work

Seventeen wetland mitigation sites in eastern Nebraska were evaluated, by vegetative zone, to assess the relative success of active and passive wetland vegetation establishment techniques. For sites with available records of species introduced, 46% of the seeded species and 31% of the transplanted species were successfully established suggesting that the intentional introduction of species (i.e. active methods) provides some degree of success in wetland creation. No significant differences were observed within or among active or passive methods for Species Richness (S), Shannon-Wiener diversity (H′), or the Floristic Quality Index (FQI) (Kruskall-Wallis test P < 0.05). However, while not statistically significant, general trends showed that, in the temporarily flooded zones, seeding resulted in both the highest overall plant diversity and highest FQI (S = 20.2, H′ = 1.74, FQI = 8.99) and, among species with cover values > 0.5%, the lowest percent non-native species (6.2%). …

Optimality In A Partitioned Task Performed By Social Insects, Jerome J. Howard

Biological Sciences Faculty Publications

Biologists have long been aware that adaptations should not be analysed in isolation from the function of the whole organism. Here, we address the equivalent issue at the scale of a social insect colony: the optimality of component behaviours in a partitioned sequence of tasks. In colonies of Atta colombica, a leaf-cutting ant, harvested leaf tissue is passed from foragers to nest workers that distribute, clean, shred and implant the tissue in fungal gardens. In four laboratory colonies of A. colombica, we found that the highest colony-wide rate of leaf tissue processing in the nest was achieved when leaf fragment …

Disturbance As Restoration In The Intermountain Sagebrush Steppe: Effects On Non Target Bird Species, Russell Edward Norvell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Changes in shrubsteppe passerine bird habitat associations in response to disturbance were investigated at multiple temporal and spatial scales. Spatial measures incorporated the effects of area at different ecological scales (nest site, territory, and landscape) to include ecologically meaningful extents. Temporal measures included seasonal and annual effects, and were designed to detect lagged responses should they occur. Local-to-landscape scale effects of mechanical restoration treatments on local extirpation and abundances of nine species indicated most were insensitive to changes in habitat quality, while abundance models showed only broad declines. Changing the availability of nesting habitat on both the attractiveness and quality …

Mountain Pine Beetle Fecundity And Offspring Size Differ Among Lodgepole Pine And Whitebark Pine Hosts, Donovan Gross

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Whitebark pine (Pinus albicaulis Engelmann) is a treeline species in the central Rocky Mountains. Its occupation of high elevations previously protected whitebark pine from long-term mountain pine beetle outbreaks. The mountain pine beetle, however, is currently reaching outbreaks of record magnitude in high-elevation whitebark pine. We used a factorial laboratory experiment to compare mountain pine beetle (Dendroctonus ponderosae Hopkins) life history characteristics between a typical host, lodgepole pine (Pinus contorta Engelmann), and whitebark pine. We tested the effects of natal host and brood host on beetle fecundity, offspring size, and brood sex-ratio. We reared mountain pine beetles …

Combining Environmental History And Soil Phytolith Analysis At The City Of Rocks National Reserve: Developing New Methods In Historical Ecology, Lesley Morris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Historical ecology is an emerging and interdisciplinary field that seeks to explain the changes in ecosystems over time through a synthesis of information derived from human records and biological data. The methods in historical ecology cover a wide range of temporal and spatial scales. However, methods for the more recent past (about 200 years) are largely limited to the human archive and dendrochronological evidence which can be subject to human bias, limited in spatial extent or not appropriate for non-forested systems. There is a need to explore new methods by which biological data can be used to understand historic vegetation …

Sex-Biased Predation On Taricha By A Novel Predator In Annadel State Park, Amber Noelle Brouillette

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Newts of the genus Taricha have long been studied due to the powerful neurotoxin found in their skin. Tetrodotoxin (TTX) acts by blocking receptors in sodium channels, ultimately resulting in death via asphyxiation. The only documented predators of species in this genus have been snakes of the genus Thamnophis. Recently, predation on Taricha in Ledson Marsh in Annadel State Park, Santa Rosa, CA was discovered. Predation was in the form of laceration or evisceration, and tracking of predation from 1998-2008 showed that it was male-biased. Two species of Taricha were found living sympatrically at this location, the California newt …