Life Sciences Commons^™

Applying Marine Protected Area Design Models In Large Estuarine Systems, Roman Zajac, Amanda E. Neely

Biology and Environmental Science Faculty Publications

Several types of design models are currently being used to develop marine protected areas (MPAs) for conservation of coastal and pelagic ecosystems. However, few studies have applied these models in large estuaries which have unique characteristics that need to be considered in MPA design, including strong physical, chemical and biological gradients and significant human impacts. We explored how one design model, MARXAN, can be applied to estuarine systems by developing MPA design scenarios for Long Island Sound, an estuary in the northeastern USA. Using sedimentary texture as a proxy for habitats, we modeled and tested several scenarios where conservation goals …

Ngasp - The Nematode Genome Annotation Assessment Project, Avril Coghlan, Tristan J. Fiedler, Sheldon J. Mckay, Paul R. Flicek, Todd W. Harris, Darin Blasiar, Lincoln D. Stein

Biomedical Engineering and Sciences Faculty Publications

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. Results: The most accurate gene-finders were …

Why Do Dolphins Carry Sponges?, Janet Mann, Brooke L. Sargeant, Jana J. Watson-Capps, Quincy A. Gibson, Michael R. Heithaus, Richard C. Connor, Eric Patterson

Department of Biological Sciences

Tool use is rare in wild animals, but of widespread interest because of its relationship to animal cognition, social learning and culture. Despite such attention, quantifying the costs and benefits of tool use has been difficult, largely because if tool use occurs, all population members typically exhibit the behavior. In Shark Bay, Australia, only a subset of the bottlenose dolphin population uses marine sponges as tools, providing an opportunity to assess both proximate and ultimate costs and benefits and document patterns of transmission. We compared sponge-carrying (sponger) females to non-spongecarrying (non-sponger) females and show that spongers were more solitary, spent …

Changes In Biotic And Abiotic Processes Following Mangrove Clearing, Elise Granek, Benjamin I. Ruttenberg

Biological Sciences

Mangrove forests, important tropical coastal habitats, are in decline worldwide primarily due to removal by humans. Changes to mangrove systems can alter ecosystem properties through direct effects on abiotic factors such as temperature, light and nutrient supply or through changes in biotic factors such as primary productivity or species composition. Despite the importance of mangroves as transitional habitats between land and sea, little research has examined changes that occur when they are cleared. We examined changes in a number of biotic and abiotic factors following the anthropogenic removal of red mangroves (Rhizophora mangle) in the Panamanian Caribbean, including …

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

Biology Faculty Publications and Presentations

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 …

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. & …

Current State Of Conservation Knowledge On Threatened Amphibian Species In Peru, Rudolf Von May, Alessandro Catenazzi, Ariande Angulo, Jason L. Brown, Jorge Carrillo, German Chavez, Jesus H. Cordova, Aleyda Curo, Amanda Delgado, Marco A. Enciso, Roberto Gutierrez, Edgar Lehr, Jorge L. Martinez, Margarita Medina-Muller, Alfonso Miranda, Daniel R. Neira, Jose A. Ochoa, Aaron J. Quiroz, Daniel A. Rodriguez, Lily O. Rodriguez, Antonio W. Salas, Tracie Seimon, Anton Seimon, Karen Siu-Ting, Juana Suarez, Claudia Torres, Evan Twomey

Department of Biological Sciences

This study documents the current state of conservation knowledge on threatened amphibian species in Peru. Following the International Union for the Conservation of Nature (IUCN) classification system, we considered species in the following categories: Critically Endangered, Endangered, Vulnerable, and Near Threatened. Even though only the first three categories are regarded as threatened by IUCN, we included the fourth category to make comparisons with the list of threatened species issued by the Peruvian government. We used the Global Amphibian Assessment's database and the list issued in Peru for this comparison. We conducted separate field surveys in 17 regions of Peru to …

Comparison Of Fish Assemblages In Two Littoral Habitats In A Neotropical Morichal Stream In Venezuela, Carmen G. Montaña, Craig A. Layman, Donald C. Taphorn

Department of Biological Sciences

Morichales are lowland streams in South American savannas with riparian forest dominated by the moriche palm (Mauritia flexuosa). We sampled littoral habitats from ten flooded vegetated patches (dominated by Mauritiella aculeate) and six sand banks in two months of the dry season (Feb-Mar 2005) in a stream in the savannas of Apure State, Venezuela. We collected samples that compromised 12,407 individual fishes of 107 species. Small-bodied fishes (< 100 mm), representing diverse trophic and life history strategies, were abundant. The most abundant species were in the families Characidae and Cichlidae. Fish assemblages from flooded vegetated patches differed significantly from those on adjacent sand banks. High structural complexity along vegetated shoreline habitats of morichal streams likely contributes to species richness and affects assemblage composition.

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 …

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 …

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.

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.

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.

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 …

The Role Of Causal Processes In The Neutral And Nearly Neutral Theories, Michael R. Dietrich, Roberta L. Millstein

Dartmouth Scholarship

The neutral and nearly neutral theories of molecular evolution are sometimes characterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory explicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. A narrow focus on outcomes obscures the significant role of weakly selected causal processes in the nearly neutral theory.

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 …

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 …

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 …

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 …

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 …

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; …

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 …

Phylogeography Of The Bigeye Chub Hybopsis Amblops (Teleostei: Cypriniformes): Early Pleistocene Diversification And Post‐Glacial Range Expansion, Peter B. Berendzen, Tony Gamble, Andrew M. Simons

Biological Sciences Faculty Research and Publications

The bigeye chub, Hybopsis amblops, is a member of the Central Highlands ichthyofauna of eastern North America. Phylogenetic analyses of the H. amblops species group based on a 1059 bp fragment of the mitochondrial DNA cytochrome b gene did not recover a monophyletic group. The inclusion of Hybopsis hypsinotus in the species complex is questionable. Within H. amblops, five strongly supported clades were identified; two clades containing haplotypes from the Ozark Highlands and three clades containing haplotypes from the Eastern Highlands and previously glaciated regions of the Ohio and Wabash River drainages. Estimates of the timing of divergence …

Living Where The Flow Is Right: How Flow Affects Feeding In Bryozoans, Marney C. Pratt

Biological Sciences: Faculty Publications

Bryozoans are suspension feeding colonial animals that remain attached to the substratum or other surfaces. How well a bryozoan can feed in a particular flow regime could help determine the distribution and abundance of that bryozoan. I tested how velocity of flow affects feeding rate in four species of bryozoans in the laboratory and how these species perform in different flow regimes in the field. I found that one species, Membranipora membranacea, had a higher ingestion rate than did the other three species at all velocities of flow tested. Membranipora also had a higher rate of ingestion at intermediate velocities, …

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 …

Molecular Characterisation Of A Bovine-Like Rotavirus Detected From A Giraffe, Emily Mulherin, Jill Bryan, Marijke Beltman, Luke O'Grady, Eugene Pidgeon, Lucie Garon, Andrew Lloyd, John Bainbridge, Helen O'Shea, Paul Whyte, Séamus Fanning

Department of Biological Sciences Publications

Background

Rotavirus (RV), is a member of the Reoviridae family and an important etiological agent of acute viral gastroenteritis in the young. Rotaviruses have a wide host range infecting a broad range of animal species, however little is known about rotavirus infection in exotic animals. In this paper we report the first characterisation of a RV strain from a giraffe calf.

Results

This report describes the identification and detailed molecular characterisation of a rotavirus strain detected from a 14-day-old Giraffe (Giraffa camelopardalis), presenting with acute diarrhea. The RV strain detected from the giraffe was characterized molecularly as G10P[11]. …

Melanocytes In The Developing And Adult Atrioventricular Valves Of The Murine Heart, Flavia Carneiro Brito

FIU Electronic Theses and Dissertations

The Neural Crest (NC) is a multipotential group of cells that arises from the dorsal aspect of the neural tube early in development. It is well established that a group of NC cells named Cardiac Neural Crest (CNC) migrates to the heart and plays a critical role in the remodeling of the aortic arch arteries and septation of the outflow tract. In this study, using the mouse mutant Pax3^sp/sp that has CNC deficits I have identified a putative novel role for the CNC in regulating apoptosis in the atrioventricular (AV) endocardial cushion. The AV endocardial cushion undergoes remodeling to …