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Assessing Causes Of Change In The Freshwater Mussels (Bivalvia: Unionidae) In The Black River, Ohio, Mark S. Lyons, Robert A. Krebs, Jeremy P. Holt, Louie J. Rundo, W. Zawiski

Biological, Geological, and Environmental Faculty Publications

Habitat destruction is believed to be the number one cause of the decline in unionid mussels. Around the world, cities, towns and agriculture alter the structure of watersheds, and the Black River in Ohio may be a typical example. We investigated the diversity and abundance of unionid mussels in this watershed and compared results to urbanization locations, to site-specific appearance of the habitat and to a 1997 fish survey, as host species are another factor important to the distribution of unionid mussels. Although shells were found for 21 species, only 11 of these species were found alive. Seven of the …

Comparison Of C. Elegans And C. Briggsae Genome Sequences Reveals Extensive Conservation Of Chromosome Organization And Synteny, Ladeana W. Hiller, Raymond D. Miller, Scott Everet Baird, Asif Chinwalla, Lucinda A. Fulton, Daniel C. Koboldt, Robert H. Waterston

Biological Sciences Faculty Publications

To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic …

Present Effects Of Past Wildfires On The Diets Of Stream Fish, Peter Koetsier, Quenton Tuckett, Joshua White

Biology Faculty Publications and Presentations

We investigated present indirect effects from a decade-old burn on the diets of stream fish. Based on soil instability and burn patterns from a 12–14-year-old wildfire complex, we separated 9 streams into 3 conditions: unburned, burned, and burned/scoured (i.e., experiencing a massive scour event 1 year post-burn). In the streams, we measured light levels and water temperatures, and we estimated fish density and biomass. We removed the digestive tracts from 9–15 rainbow trout (Oncorhynchus mykiss) from each stream and used a gravimetric procedure to analyze gut contents. Canopy cover development may dictate the composition of dietary items. Greater …

Direct And Indirect Effects Of Animal Detritus On Growth, Survival, And Mass Of Invasive Container Mosquito Aedes Albopictus (Diptera : Culicidae, Donald A. Yee, Banugopan Kesavaraju, Steven A. Juliano

Faculty Publications – Biological Sciences

Compared with plant detritus, animal detritus yields higher growth rates, survival, adult mass, and population growth of container-dwelling mosquitoes. It is unclear whether the benefit from animal detritus to larvae results from greater microorganism growth, direct ingestion of animal detritus by larvae, or some other mechanism. We tested alternative mechanisms by which animal detritus may benefit the invasive container-dwelling mosquito Aedes albopictus (Skuse) (Diptera: Culicidae). In the laboratory, larvae were reared under three conditions with access to 1) detritus, but where microorganisms in the water column were reduced through periodic flushing; 2) water column microorganisms, but larvae had no direct …

Comparative Functional Analysis Of Aquaporins/Glyceroporins In Mammals And Anurans, Carissa M. Krane, David L. Goldstein

Biology Faculty Publications

Maintenance of fluid homeostasis is critical to establishing and maintaining normal physiology. The landmark discovery of membrane water channels (aquaporins; AQPs) ushered in a new area in osmoregulatory biology that has drawn from and contributed to diverse branches of biology, from molecular biology and genomics to systems biology and evolution, and from microbial and plant biology to animal and translational physiology. As a result, the study of AQPs provides a unique and integrated backdrop for exploring the relationships between genes and genome systems, the regulation of gene expression, and the physiologic consequences of genetic variation. The wide species distribution of …

Prevalence And Diversity Of Avian Hematozoan Parasites In Asia: A Regional Study, Farah Ishtiaq, Eben Gering, Jon H. Rappole, Asad R. Rahmani, Yadvendradev V. Jhala, Carla J. Dove, Christopher M. Milensky, Storrs L. Olson, Mike A. Peirce, Robert C. Fleischer

Biology Faculty Articles

Tissue samples from 699 birds from three regions of Asia (Myanmar, India, and South Korea) were screened for evidence of infection by avian parasites in the genera Plasmodium and Haemoproteus. Samples were collected from November 1994 to October 2004. We identified 241 infected birds (34.0%). Base-on-sequence data for the cytochrome b gene from 221 positive samples, 34 distinct lineages of Plasmodium, and 41 of Haemoproteus were detected. Parasite diversity was highest in Myanmar followed by India and South Korea. Parasite prevalence differed among regions but not among host families. There were four lineages of Plasmodium and one of …

Lifetime Reproductive Success Of Female Eastern Kingbirds (Tyrannus Tyrannus): Influence Of Lifespan, Nest Predation And Body Size, Michael T. Murphy

Biology Faculty Publications and Presentations

I report on the lifetime reproductive success (LRS) of female Eastern Kingbirds (Tyrannus tyrannus) in central New York. I investigated the major correlates of LRS and specifi cally tested the hypothesis that small body size yields reproductive benefi ts. Lifetime reproductive success varied widely: 15–20% of females failed to fledge young over their life, whereas 50% of young were fledged by 20% of females. Female lifespan varied between one and eight years, and females that died after one breeding season tended to be smaller-bodied than long-lived females (≥2 seasons). I therefore conducted analyses of LRS for the entire sample and …

Sensory Modulation Of Crustacean Non-Giant Tailflipping, Sandra Y. Espinoza, Zen Faulkes

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

As a first step in re-examining the modulation of non-giant tailflipping, we further investigate how the presence of weapons affects non-giant tailflipping. Removing both claws significantly changes the threshold for tailflipping (Krasne and Wine, 1975; Lang et al., 1977). Claw removal affects several variables at once, however; e.g., the animal’s mass; visual stimuli associated with having claws; tactile and proprioceptive cues. For example, a crayfish with claws that are present but useless might “bluff,” and may not tailflip away from a stimuli more than an intact animal.

Atplai Is An Acyl Hydrolase Involved In Basal Jasmonic Acid Production And Arabidopsis Resistance To Botrytis Cinerea, Xuemin Wang, Wenyu Yang, Shivakumar Devaiah, Xiangqing Pan, Giorgis Isaac, Ruth Welti

Biology Department Faculty Works

Intracellular phospholipase A2 (PLA2) plays an important role in regulating oxylipin biosynthesis in mammals, but the molecular and biochemical nature of intracellular PLA2 is not well understood in plants. Arabidopsis thaliana gene At1g61850 (AtPLAI) encodes a 140-kDa protein that is most similar to mammalian calcium-independent PLA2, and additionally contains leucine-rich repeats and Armadillo repeats. AtPLAI hydrolyzes phospholipids at both the sn-1 and sn-2 positions, but prefers galactolipids to phospholipids as substrates. Profiling of lipid species altered in response to the necrotrophic fungus Botrytis cinerea revealed decreases in the levels of phosphatidylglycerol and digalactosyldiacylglycerol, suggesting that hydrolysis of plastidic polar lipids …

Seed Dispersal Limitation In A Neotropical Nutmeg, Virola Flexuosa (Myristicaceae): An Ecological And Genetic Approach, Kimberly Mae Holbrook

Dissertations

Seed dispersal contributes significantly to tropical forest maintenance, influencing processes, such as metapopulation dynamics and population persistence. Although several hypotheses have been debated regarding the contribution of seed dispersal to tropical forest diversity, recent work suggests that dispersal limitation is a major component in determining plant population patterns. This dissertation research broadly addresses hypotheses that seed dispersal behaviour of frugivores influences dispersal limitation of a Neotropical tree, Virola flexuosa (Myristicaceae). To test these hypotheses, I studied how different frugivores influenced seed dispersal of V. flexuosa at two sites in Amazonia Ecuador. General research objectives were to estimate fruit removal by …

Rhizobium Etli Ce3 Bacteroid Lipopolysaccharides Are Structurally Similar But Not Identical To Those Produced By Cultured Ce3 Bacteria, Wim D'Haeze, Christine Leoff, Glenn Freshour, K. Dale Noel, Russell W. Carlson

Biological Sciences Faculty Research and Publications

Rhizobium etli CE3 bacteroids were isolated from Phaseolus vulgaris root nodules. The lipopolysaccharide (LPS) from the bacteroids was purified and compared with the LPS from laboratory-cultured R. etli CE3and from cultures grown in the presence of anthocyanin. Comparisons were made of the O-chain polysaccharide, the core oligosaccharide, and the lipid A. Although LPS from CE3 bacteria and bacteroids are structurally similar, it was found that bacteroid LPS had specific modifications to both the O-chain polysaccharide and lipid A portions of their LPS. Cultures grown with anthocyanin contained modifications only to the O-chain polysaccharide. The changes to the O-chain polysaccharide consisted …

A Hybrid First Year Science Course For Engineering Students – Integrating Biology With Chemistry, David Harding, Pauline Schwartz, Jean Nocito-Gobel, Agamemnon Koutsospyros

Civil Engineering Faculty Publications

Biology is playing an increasingly important role in many engineering fields. With the typical engineering program already having a high credit hour requirement, the question becomes, how to best integrate biology concepts into a packed engineering curriculum. A typical biology course is not likely to introduce the important concepts of biology to engineering students. The solution here is to develop a hybrid course that integrates chemistry and biology. In the course, Chemistry with Applications to Biosystems, the concept is to develop a course that integrally links important concepts of chemistry and biology. The course focuses on the areas of biology …

A Versatile Computational Pipeline For Bacterial Genome Annotation Improvement And Comparative Analysis, With Brucella As A Use Case, Gongxin Yu, Eric E. Snyder, Stephen M. Boyle, Oswald R. Crasta, Michael Czar, Shrinivasrao P. Mane, Anjan Purkayastha, Bruno Sobral, João C. Setubal

Biology Faculty Publications and Presentations

We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar’s capabilities by presenting results from the analysis …

The Effects Of Testosterone On The Induction Of Experimental Autoimmune Thyroiditis In Sprague-Dawley Rats, Travis William Reed

Theses, Dissertations and Culminating Projects

Experimental Autoimmune Thyroiditis (EAT) could not be induced in young, immature Sprague-Dawley rats (150-200g). EAT was successfully induced in the same group of animals when they weighed 400g. The animals developed the disease every time. Sexual immaturity or immaturity of the immune system may be responsible for these results (Fernandez, 2006). It has been proven that pharmacologic doses of testosterone have shown immunosuppressive effects on the severity of EAT in the PVG/c strain of rats (Ahmed et al, 1982). In this current thesis research, it appears that normal physiologic levels of testosterone have no effect on the development and severity …

Structure-Function Studies Of Self- Assembling Flagellin Proteins Fromsalmonella Typhimurium And Aquifex Pyrophilus, Venkata Raghu Ram Malapaka

Dissertations

The eubacterial flagellum is a complex structure with an elongated extracellular filament that is primarily composed of a single protein termed flagellin. The highly conserved N-and C- termini of flagellin are important in its export and assembly, whereas the middle "hypervariable" region is highly variable in size across different species and is largely dispensable. InSalmonella typhimurium phase 1 flagellin (FliC), this hypervariable region encodes two solvent-exposed D2 and D3 domains. The functional role of this knob-like structural feature in motility remains unclear. The structural and physiological role of the hypervariable region in flagellar assembly, stability and cellular motility was investigated. …

Preferential Myosin Heavy Chain Isoform B Expression May Contribute To The Faster Velocity Of Contraction In Veins Versus Arteries, Catherine M. Rondelli, Irina T. Szasz, Anas Kayal, Keshari Thakali, Ralph E. Watson, Arthur S. Rovner, Thomas J. Eddinger, Gregory D. Fink, Stephanie W. Watts

Biological Sciences Faculty Research and Publications

Smooth muscle myosin heavy chains occur in 2 isoforms, SMA (slow) and SMB (fast). We hypothesized that the SMB isoform is predominant in the faster-contracting rat vena cava compared to thoracic aorta. We compared the time to half maximal contraction in response to a maximal concentration of endothelin-1 (ET-1; 100 nM), potassium chloride (KCl; 100 mM) and norepinephrine (NE; 10 µM). The time to half maximal contraction was shorter in the vena cava compared to aorta (aorta: ET-1 = 235.8 ± 13.8 s, KCl = 140.0 ± 33.3 s, NE = 19.8 ± 2.7 s; vena cava: ET-1 = 121.8 …

Status And Distribution Of Manatees In Honduras And The Use Of Side-Scan Sonar, Daniel Gonzalez-Socoloske

Loma Linda University Electronic Theses, Dissertations & Projects

All manatee species are listed as endangered or vulnerable. Studying these animals is very challenging because of their reticent behavior and the remote and complex habitats in which they are found. This study dealt with three challenges in manatee conservation: identification of hotspots, manatee detection in turbid and tannin-stained waters, and regional collaboration between countries. Using the West Indian Manatee (Trichechus manatus) as the study subject, these three challenges were examined and possible solutions were presented.

The distribution of manatees in Honduras is known from sporadic death reports and informal interviews. Like many other countries in Mesoamerica, Honduras had …

Barriers To Flow: The Effects Of Experimental Cage Structures On Water Velocities In High-Energy Subtidal And Intertidal Environments, Luke P. Miller, Brian Gaylord

Faculty Publications, Biological Sciences

For decades, marine ecologists have used cages as biological enclosure or exclosure devices to manipulate movement, growth, and survival of organisms. The ability to control the densities of focal organisms makes these structures a powerful tool. However, cages can often produce artifacts that influence the outcome of experiments. Although a subset of these artifacts have been examined previously, the effects of cages on water motion have not been adequately addressed from a quantitative standpoint, especially in high-flow environments. We targeted this data gap by explicitly measuring the fractional degree of velocity reduction inside a variety of experimental cage structures across …

Neural Defects And Cardiac Arrhythmia In Fish Larvae Following Embryonic Exposure To 2,2',4,4'-Tetrabromodiphenyl Ether (Pbde 47), Sean C. Lema, Irvin R. Schultz, Nathaniel L. Scholz, John P. Incardona, Penny Swanson

Biological Sciences

Polybrominated diphenyl ethers (PBDEs) are added to plastics, polyurethane foam, and textiles as a flame retardant. While PBDEs play a key role in reducing loss of human life and property from fires, these flame retardants have become pervasive organic contaminants in the environment and in the tissues of fish, birds, marine mammals, and humans. Levels of PBDEs in wildlife and humans continue to rise, raising concerns about potential ecological and health risks associated with exposure to these chemicals. Nevertheless, there is little currently known about the toxicological effects of PBDE exposure. Here, we examined the developmental toxicity of the PBDE …

Coordinated Regulation Of Myc Trans-Activation Targets By Polycomb And The Trithorax Group Protein Ash1, Julie M. Goodliffe, Michael D. Cole, Eric Wieschaus

Dartmouth Scholarship

The Myc oncoprotein is a transcriptional regulator whose function is essential for normal development. Myc is capable of binding to 10% of the mammalian genome, and it is unclear how a developing embryo controls the DNA binding of its abundant Myc proteins in order to avoid Myc's potential for inducing tumorigenesis.To identify chromatin binding proteins with a potential role in controlling Myc activity, we established a genetic assay for dMyc activity in Drosophila. We conducted a genome-wide screen using this assay, and identified the Trithorax Group protein Ash1 as a modifier of dMyc activity. Ash1 is a histone methyltransferase known …

Influence Of Juvenile Hormone On Territorial And Aggressive Behavior In The Painted Lady (Vanessa Cardui) And Eastern Black Swallowtail (Papilio Polyxenes), Tara Bergin

Honors Theses

Competition is important in environments with limited resources. Males of many insect species are territorial and will defend resources, such as a food source or egg-laying site, against intruders, or even compete to attract a mate. In insects, evidence suggests that juvenile hormone acts as an aggression mediator, much like testosterone in other animal species. In this study I tested this idea using a group of male Painted Lady butterflies, Vanessa cardui, and Eastern Black Swallowtail butterflies, Papilio polyxenes, that were treated prior to metamorphosis with either a high or low dose of methoprene acid (a juvenile hormone mimic). Male-male …

Comparative Immune Function In Wild Birds, Kevin David Matson

Dissertations

Over the last several decades, interest in quantifying immune function in comparative studies of wild animals has grown appreciably. Now, the field of ecological immunology is undergoing a transition, and ¿second generation¿ studies are being designed and carried out. With a greater appreciation of the complexity of immune systems, these second generation studies are commonly distinguished from their antecedents by making comparisons using multiple assays and including multiple species. I worked to advance this transition by developing novel approaches to comparative immunology, exploring the interrelationships among indices of immune function, and applying multiple indices to a question of comparative avian …

The Role Of Local And Regional Factors In The Foraging Ecology Of Birds Associated With Polylepis Woodlands, Grace Patricia Servat-Valenzuela

Dissertations

Understanding the extent to which patterns of functional structure are repeated in space and the scale at which different factors (local and regional) operate to explain community patterns are of important in community ecology. I studied the extent of spatial variation in foraging ecology of birds in the Polylepis community, a vegetation system of the Andes, in regard to variation in local (vegetation structure, floristic composition, food resources) and regional factors (biogeography). Specifically, I studied foraging ecology of nine insectivorous bird species (and the assemblage they conform) across twelve disjunct woodlands embedded in three biogeographic regions of the Peruvian Andes. …

Histologic Examination Of Host-Parasite Interactions In The Gulf Killifish, Fundulus Grandis, Marlee Marsh

All Dissertations

Little is known about the immunobiology of fish responses to parasitic infections. The aim of this study was to describe a model for the examination of fish-nematode interactions on the immunological front, and to develop new reagents for the study of this model. Gulf killifish, Fundulus grandis, were collected over two seasons from Simmon's Bayou, Jackson County, MS, USA, pre Hurricane Katrina, and examined for endoparasites, particularly the larval nematode Eustrongylides ignotus. A baseline study was preformed to determine the prevalence, intensity, and histologic features of E. ignotus infection in F. grandis, and this study serves as the first description …

Myosin Ii Isoforms In Smooth Muscle: Heterogeneity And Function, Thomas J. Eddinger, Daniel P. Meer

Biological Sciences Faculty Research and Publications

Both smooth muscle (SM) and nonmuscle class II myosin molecules are expressed in SM tissues comprising hollow organ systems. Individual SM cells may express one or more of multiple myosin II isoforms that differ in myosin heavy chain (MHC) and myosin light chain (MLC) subunits. Although much has been learned, the expression profiles, organization within contractile filaments, localization within cells, and precise roles in various contractile functions of these different myosin molecules are still not well understood. However, data supporting unique physiological roles for certain isoforms continues to build. Isoform differences located in the S1 head region of the MHC …

Dislodged But Not Dead: Survivorship Of A High Intertidal Snail Following Wave Dislodgement, Luke P. Miller, Michael J. O'Donnell, Katharine J. Mach

Faculty Publications, Biological Sciences

Waves breaking on rocky shorelines impart large forces on intertidal organisms, sometimes dislodging individuals. Dislodged individuals may be deposited in habitats that have a greater risk of predation or that prevent return to preferred regions on the shore. Thus, dislodgement is often assumed to be lethal. We experimentally dislodged Littorina keenae snails from high in the intertidal zone to test the likelihood of survival. Under a variety of wave conditions, we measured return rates to the high shore of 54–90%, so in this species, dislodgement is not equal to death. Snails showed a strong preference for returning to the approximate …

A Historic Perspective: The Response Of Breeding Passerines To Rangeland Alteration In Rich County, Utah, Lindsay J. Brown

Biology

Shrub-dominated ecosystems on private lands are important rangeland resources through much of the western U.S., including Rich County, Utah. Because of its important role in livestock production, this shrubsteppe ecosystem has been exposed to a variety of sagebrush removal methods. Little is known about the relative effects of chemical, mechanical, or burn treatments on breeding passerine communities. Furthermore, most studies address only short-term effects. We studied breeding passerine communities and vegetation on 17 untreated sites and 49 range sites treated between 1962 and 2004 to examine the effects of treatment type and treatment age. The sagebrush treatments produced considerable changes …

Effects Of Environmental Conditions And Insect Life Stages On Performance Of Entomopathogenic Nematodes For Suppression Of Plum Curculio, Conotrachelus Nenuphar (Coleoptera: Curculionidae), In Northern Utah, Hong Geun Kim

Biology

In a series of field and laboratory experiments, I tested two entomopathogenic nematode species, two nematode concentrations, and three life stages of the economically damaging insect pest, Contrachelus nenuphar, to support the development of a biological control program for this pest in northern Utah. Two entomopathogenic nematodes, Heterorhabditis bacteriophora and Steinernema feltiae, were tested for their virulence. The population of H. bacteriophora tested was collected from soil infested with plum curculio in Brigham City, UT in 2002. The S. feltiae population was obtained from a commercial source. In temperature bioassays, the two nematodes species exhibited different thermal ranges. …

The Role Of Individual-Level Behavior: From Safe Passage To Self-Organization, Bertrand H. Lemasson

Biology

A considerable amount of research in fisheries exists to assess and predict the success rate of fish attempting to navigate through artificial barriers in their environment. Such barriers typically include dams, culverts, power plants, and pumping stations. This dissertation contributes to fisheries science, and general ecology, by determining how individual-level behavior affects the movement decisions of solitary fish and how simple inter-individual interactions can generate complex forms of collective behavior. The current research improves our ability to model small-scale movement patterns, such as those expected within the artificial restrictions of a water diversion facility, and provides insight into the communication …

Proteomic And Immunoblot Analyses Of Bartonella Quintana Total Membrane Proteins Identify Antigens Recognized By Sera From Infected Patients, Jenni K. Boonjakuakul, Helen L. Gerns, Yu-Ting Chen, Linda D. Hicks, Michael F. Minnick, Scott E. Dixon, Steven C. Hall, Jane E. Koehler

Biological Sciences Faculty Publications

Bartonella quintana is a fastidious, gram-negative, rod-shaped bacterium that causes prolonged bacteremia in immunocompetent humans and severe infections in immunocompromised individuals. We sought to define the outer membrane subproteome of B. quintana in order to obtain insight into the biology and pathogenesis of this emerging pathogen and to identify the predominant B. quintana antigens targeted by the human immune system during infection. We isolated the total membrane proteins of B. quintana and identified 60 proteins by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and peptide mass fingerprinting. Using the newly constructed proteome map, we then utilized two-dimensional immunoblotting with sera from …