Digital Commons Network^™

Phylogeographic And Phylogenetic Exploration Of Plethodon (Plethodontidae, Caudata) Salamanders In The Pacific Northwest, Tara Anne Pelletier

Dissertations and Theses

Genetic studies of amphibians often reveal substantial population structure due to either historical demographics from changing climate and geographic features over varying timeframes. Eight species of terrestrial salamanders (Family: Plethodontidae, Genus: Plethodon) reside in forests of the Pacific Northwest (PNW). Plethodon vehiculum is the most widespread and abundant terrestrial salamander in the PNW yet evolutionary studies are lacking. Using mitochondrial DNA (mtDNA) sequence data (D-loop and cytb) questions regarding the phylogeography of P. vehiculum and phylogenetics of western Plethodons are explored. Two major clades were defined in P. vehiculum, a southern clade in the Klamath-Siskiyou region and a …

Andrews Student Awarded Goldwater Scholarship, Keri Suarez

Lake Union Herald

No abstract provided.

Inhibition Of Aβ42 Aggregation Using Peptides Selected From Combinatorial Libraries, Michael Baine, Daniel S. Georgie, Elelta Z. Shiferraw, Theresa P. T. Nguyen, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

Increasing evidence suggests that the aggregation of the small peptide Aβ42 plays an important role in the development of Alzheimer’s disease. Inhibiting the initial aggregation of Aβ42 may be an effective treatment for preventing, or slowing, the onset of the disease. Using an in vivo screen based on the enzyme EGFP, we have searched through two combinatorially diverse peptide libraries to identify peptides capable of inhibiting Aβ42 aggregation. From this initial screen, three candidate peptides were selected and characterized. ThT studies indicated that the selected peptides were capable of inhibiting amyloid aggregation. Additional ThT studies showed that one of the …

The Relationship Between Plasma Steroid Hormone Concentrations And The Reproductive Cycle Of The Northern Pacific Rattlesnake, Crotalus Oreganus, Craig Michael Lind

Master's Theses

To gain a better understanding of the role of steroid hormones in vertebrate reproduction, we quantified steroid hormone concentrations in a free ranging population of the Northern Pacific rattlesnake, Crotalus oreganus. Plasma steroid hormone concentrations were quantified for both male and female snakes throughout the active season (Mar-Oct). We measured testosterone (T), 5α-dihydrotestosterone (DHT), and corticosterone (B) concentrations in male and female snakes. 17β-estradiol (E2) and progesterone (P) were measured in females only. We also observed breeding behaviors (e.g. consortship, courtship, and copulation) in the field and measured testis and follicle size in male and female snakes from museum collections. …

Investigating The Roles Of Ndj1 And Tid1 In Distributive Segregation Using Non-Exchange Chromosomes, Jonathan V. Henzel

Master's Theses

Meiosis is a specialized cell division that leads to a reduction of ploidy in sexually reproducing organisms through segregation of homologous chromosomes at the first meiotic division. Improper segregation of chromosomes during meiosis results in anueploidy, which is usually fatal during embryonic development. The meiotic process is therefore tightly regulated. Typically, proper segregation of homologs at meiosis I requires pairing of homologous chromosomes, followed by crossover recombination between homologs. Crossovers enable proper chromosomal segregation during the first meiotic division in part by establishing tension in the meiotic spindle. However, in the absence of crossovers, some cells maintain the ability to …

Spatial, Seasonal, And Size-Dependent Variation In The Diet Of Sacramento Pikeminnow In The Main Stem Of Chorro Creek, Central Coast California, Brian G. Dugas

Master's Theses

This study examined the diet composition of ninety-nine Sacramento pikeminnow (150-410 mm [5.9-16 in] fork length [FL]) collected from the upper and lower main stem of Chorro Creek, Morro Bay Watershed, California in 2006. The goal of this study was to characterize the spatial and seasonal variability in the diet of Sacramento pikeminnow within Chorro Creek and to determine what proportion of the diet is represented by rainbow trout (Oncorhynchus mykiss) and their anadromous form (steelhead). Prey was identified in 88% of the samples collected in the early season and 84% of the samples collected in the late season. Fish …

Biological Effects Within No-Take Marine Reserves: A Global Synthesis, Sarah E. Lester, Benjamin S. Halpern, Kirsten Grorud-Colvert, Jane Lubchenco, Benjamin I. Ruttenberg, Steven D. Gaines, Satie Airamé, Robert R. Warner

Biological Sciences

The study and implementation of no-take marine reserves have increased rapidly over the past decade, providing ample data on the biological effects of reserve protection for a wide range of geographic locations and organisms. The plethora of new studies affords the opportunity to reevaluate previous findings and address formerly unanswered questions with extensive data syntheses. Our results show, on average, positive effects of reserve protection on the biomass, numerical density, species richness, and size of organisms within their boundaries which are remarkably similar to those of past syntheses despite a near doubling of data. New analyses indicate that (1) these …

Effects Of Experience On Maternal Behavior In Belding’S Ground Squirrels (Spermophilus Beldingi): Older And Wiser?, Mikael Langner

Master's Theses

Maternal behavior is an important behavior because it influences whether or not raising one’s offspring is successful. Maternal experience is positively correlated with successful maternal behavior. This association is evident when comparing first-time mothers with mothers who have prior experience raising young. Life experience not related to raising young can also positively influence maternal behavior. In this work, the hypothesis that is tested is whether or not maternal experience enhances the ability of a female to assess the threat level of a situation. The model species used to conduct the study is the Belding ground squirrel (Spermophilus beldingi), …

Activity And Interactions Of Liposomal Antibiotics In Presence Of Polyanions And Sputum Of Patients With Cystic Fibrosis, Misagh Alipour, Zacharias E. Suntres, Majed Halwani, Ali Azghani, Abdelwahab Omri

Biology Faculty Publications and Presentations

Background: To compare the effectiveness of liposomal tobramycin or polymyxin B against Pseudomonas aeruginosa in the Cystic Fibrosis (CF) sputum and its inhibition by common polyanionic components such as DNA, F-actin, lipopolysaccharides (LPS), and lipoteichoic acid (LTA). Methodology: Liposomal formulations were prepared from a mixture of 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) or 1,2-Dipalmitoyl-sn-Glycero-3-Phosphocholine (DPPC) and Cholesterol (Chol), respectively. Stability of the formulations in different biological milieus and antibacterial activities compared to conventional forms in the presence of the aforementioned inhibitory factors or CF sputum were evaluated. Results: The formulations were stable in all conditions tested with no significant differences compared to the controls. …

Insight Into The Carboxyl Transferase Domain Mechanism Of Pyruvate Carboxylase From Rhizobium Etli, Tonya N. Zeczycki, Martin St. Maurice, Sarawut Jitrapakdee, John C. Wallace, Paul V. Attwood, W Wallace Cleland

Biological Sciences Faculty Research and Publications

The effects of mutations in the active site of the carboxyl transferase domain of Rhizobium etli pyruvate carboxylase have been determined for the forward reaction to form oxaloacetate, the reverse reaction to form MgATP, the oxamate-induced decarboxylation of oxaloacetate, the phosphorylation of MgADP by carbamoyl phosphate, and the bicarbonate-dependent ATPase reaction. Additional studies with these mutants examined the effect of pyruvate and oxamate on the reactions of the biotin carboxylase domain. From these mutagenic studies, putative roles for catalytically relevant active site residues were assigned and a more accurate description of the mechanism of the carboxyl transferase domain is presented. …

Immunodeficient Mouse Strains Display Marked Variability In Growth Of Human Melanoma Lung Metastases, Beatriz M. Carreno, Joel R. Garbow, Grant R. Kolar, Erin N. Jackson, John A. Engelbach, Michelle Becker-Hapak, Leonidas N. Carayannopoulos, David Piwnica-Worms, Gerald P. Linette

Biological Sciences Faculty Research & Creative Works

Purpose: Immunodeficient mice serve as critical hosts for transplantation of xenogeneic cells for in vivo analysis of various biological processes. Because investigators typically select one or two immunodeficient mouse strains as recipients, no comprehensive study has been published documenting differences in human tumor engraftment. Taking advantage of the increased metastatic potential of RhoC-expressing human (A375) melanoma cells, we evaluate four immunodeficient mouse strains: severe combined immunodeficiency (scid), nonobese diabetic (NOD)-scid, NOD-scid β2m^null, and NOD-scid IL2Rγ;^null as xenograft tumor recipients. Experimental Design: Bioluminescence, magnetic resonance imaging, and histopathology were used to monitor serial tumor growth. Natural killer (NK) …

Contribution Of Candida Albicans To The Synthesis Of The Volatile Organic Compound Ethanol In Putrefied Bodies, Chelsey Mozingo

Honors Theses

This experiment sought to determine if Candida albicans contributed to the production of the volatile organic compound ethanol in decomposing beef livers. The results this experiment proved to be inconclusive. This experiment showed no correlation between the amount the presence of Candida albicans and the production of the volatile organic compound ethanol based on the standard addition method. This may be indicative that VOC analysis is not an appropriate method for determining time of death based on a quantitative analysis of volatile organic compounds. However, the experimental design most likely needs be altered to accommodate a more accurate method of …

Initiating Chromosome Replication In E. Coli: It Makes Sense To Recycle, Alan C. Leonard, Julia E. Grimwade

Biomedical Engineering and Sciences Faculty Publications

Initiating new rounds of Escherichia coli chromosome replication requires DnaA-ATP to unwind the replication origin, oriC, and load DNA helicase. In this issue of Genes & Development, Fujimitsu and colleagues (pp. 1221-1233) demonstrate that two chromosomal sites, termed DARS (DnaA-reactivating sequences), recycle inactive DnaA-ADP into DnaA-ATP. Fujimitsu and colleagues propose these sites are necessary to attain the DnaA-ATP threshold during normal growth and are important regulators of initiation timing in bacteria. © 2009 by Cold Spring Harbor Laboratory Press.

Identification Of Potentially Pathogenic Yeast Species In Seagull Guano By Molecular Techniques, Tobias L. Banks

Honors Theses

Although studies have been performed identifying bacteria present in seagull guano, limited studies have been done with fungi, leaving a significant gap in our knowledge of a potentially significant reservoir of human disease. If pathogenic fungi are being deposited by seagulls in their feces then it is possible that the Department of Health might elect to monitor sand, as well as water, for a broad spectrum of disease-causing microbes. Currently only water is tested for the presence of coliform bacteria. It is hypothesized that there are pathogenic yeast-like fungi present in the guano of seagulls, that these fungi are deposited …

Assesment Of Florida Bass, (Micropterus Floridanus), Stocking In Several Arkansas Lake Largemouth Bass, (M. Salmoides), Populations Using Microsatellite Analysis, Ryan Martin Allen

Student Theses and Dissertations

Arkansas largemouth bass populations have been stocked with the exotic Florida bass for several decades to enhance lake fisheries. This study sampled 1,474 bass from eight Arkansas lakes to determine the success of introducing Florida bass alleles and hybridization events between bass species. Microsatellite data was then compared to historical allozyme data. Additionally, relationships were identified between Florida bass allele frequencies and lake characteristics as well as phenotypes and condition and length at age. A wide range of Florida bass allele frequencies were identified between lakes (10 - 70%), with the most highly correlated variable for successful stocking being reservoir …

Closing The Seed Dispersal Loop For Guettarda Viburnoides (Rub.): Connecting Patterns Of Avian Seed Dispersal With Population Growth In A Neotropical Savanna, Andrea Patricia Loayza

Dissertations

This study connects data on frugivore activity, post-dispersal seed fate and plant population demography using stage-specific demographic modeling to examine the role of individual dispersers for plant population dynamics of the fleshy-fruited Neotropical tree Guettarda viburnoides (Rubiaceae) in northeastern Bolivian savannas. Detailed information on frugivory and seed dispersal of G. viburnoides reveals that the endocarps of this plant are dispersed mainly by two species of birds: Cyanocorax cyanomelas and Pteroglossus castanotis, which are defined as the quantitatively important dispersers of G. viburnoides. These two species differ in several qualitative aspects of seed dispersal: 1) They select fruits of …

Tritrophic Interactions In Forests: Direct And Indirect Interactions Between Birds, Insect Herbivores, And Oaks, Nicholas Anthony Barber

Dissertations

This study examines direct and indirect relationships between three trophic levels to determine effects on plant damage, herbivore abundance and community structure, and bird distribution in forest ecosystems. Exclusion experiments on white oak (Quercus alba) revealed that bird predation effects to not vary spatially despite variation in abundance of both birds and insects. Using a leaf quality manipulation, I demonstrated that bird impacts do not differ with host plant quality. Rather, birds and plant traits had additive effects on herbivore damage. Bottom-up effects of leaf quality were also more important than top-down effects of birds in structuring the insect herbivore …

Effects Of Estrogen On Muscle Damage In Response To An Acute Resistance Exercise Protocol, Megan R. Wolf

Honors Scholar Theses

Creatine Kinase (CK) is used as a measure of exercise-induced muscle membrane damage. During acute eccentric (muscle lengthening) exercise, muscle sarcolemma, sarcoplasmic reticulum, and Z-lines are damaged, thus causing muscle proteins and enzymes to leak into the interstitial fluid.

Strenuous eccentric exercise produces an elevation of oxygen free radicals, which further increases muscle damage. Muscle soreness and fatigue can be attributed to this membrane damage. Estradiol, however, may preserve membrane stability post-exercise (Brancaccio, Maffulli, & Limongelli, 2007; Carter, Dobridge, & Hackney, 2001; Tiidus, 2001). Because estradiol has a similar structure to Vitamin E, which is known to have antioxidant properties, …

Towards A New Developmental Synthesis: Adaptive Developmental Plasticity And Human Disease, P. D. Gluckman, M. A. Hanson, P. Bateson, A. S. Beedle, C. M. Law, Z. A. Bhutta, K. V. Snokhin, P. Bougneres, G. R. Chandak, P. Dasgupta, G. D. Smith, P. T. Ellison, T. E. Forrester, Scott F. Gilbert, E. Jablonka, H. Kaplan, A. M. Prentice, S. J. Simpson, R. Uauy, M. J. West-Eberhard

Biology Faculty Works

The Lancet has rightly drawn attention to the goals of reducing the burden of maternal and childhood undernutrition,¹ focusing mainly on short-term outcomes such as infant survival and stunting.² However, the longer term effects on adult health³ of a poor start to life suggest a further perspective. Developmental effects have been viewed traditionally in the context of major disruptions such as caused by teratogens, prematurity and growth retardation, but there is increasing appreciation of the role of developmental plasticity, which provides individuals with the flexibility to adjust their trajectory of development to match their environment.

An Examination Of The Correlation Between Shoot Apical Meristem Size And Leaf Heterophylly In Pisum Sativum, Cynthia Mary Halfman

Undergraduate Honors Thesis Collection

This study is a quantitative examination of the ramifications of leaf development as influenced by the size of the shoot apical meristem. I wish not to delve into a genetic examination of the shoot apical meristem but rather into the possible correlation between the apical meristem size and leaf heterophylly. If changes in shoot apical meristem size influence heterophylly in leaves, then as shoot apical meristem changes, leaf characteristics will change. This change may result from two different relationships.

Apicomplexan Parasites Co-Opt Host Calpains To Facilitate Their Escape From Infected Cells, Rajesh Chandramohanadas, Paul H. Davis, Daniel P. Beiting, Michael B. Harbut, Claire Darling, Geetha Velmourougane, Ming Yeh Lee, Peter A. Greer, David S. Roos, Doron C. Greenbaum

Biology Faculty Publications

Apicomplexan parasites, including Plasmodium falciparum and Toxoplasma gondii (the causative agents of malaria and toxoplasmosis, respectively), are responsible for considerable morbidity and mortality worldwide. These pathogenic protozoa replicate within an intracellular vacuole inside of infected host cells, from which they must escape to initiate a new lytic cycle. By integrating cell biological, pharmacological, and genetic approaches, we provide evidence that both Plasmodium and Toxoplasma hijack host cell calpain proteases to facilitate parasite egress. Immunodepletion or inhibition of calpain-1 in hypotonically lysed and resealed erythrocytes prevented the escape of P. falciparum parasites, which was restored by adding purified calpain-1. Similarly, efficient …

Analysis And Classification Of Sounds Produced By Asian Elephants (Elephas Maximus), Sharon Stuart Glaeser

Dissertations and Theses

Relatively little is known about the vocal repertoire of Asian elephants (Elephas maximus), and a categorization of basic call types and modifications of these call types by quantitative acoustic parameters is needed to examine acoustic variability within and among call types, to examine individuality, to determine communicative function of calls via playback, to compare species and populations, and to develop rigorous call recognition algorithms for monitoring populations.

This study defines an acoustic repertoire of Asian elephants based on acoustic parameters, compares repertoire usage among groups and individuals, and validates structural distinction among call types through comparison of manual and automated …

Isolation And Characterization Of A Spontaneously Immortalized Bovine Retinal Pigmented Epithelial Cell Line, Thomas E. Liggett, T. Daniel Griffiths, Elizabeth R. Gaillard

Biological Sciences Faculty Research and Publications

Background

The Retinal Pigmented Epithelium (RPE) is juxtaposed with the photoreceptor outer segments of the eye. The proximity of the photoreceptor cells is a prerequisite for their survival, as they depend on the RPE to remove the outer segments and are also influenced by RPE cell paracrine factors. RPE cell death can cause a progressive loss of photoreceptor function, which can diminish vision and, over time, blindness ensues. Degeneration of the retina has been shown to induce a variety of retinopathies, such as Stargardt's disease, Cone-Rod Dystrophy (CRD), Retinitis Pigmentosa (RP), Fundus Flavimaculatus (FFM), Best's disease and Age-related Macular Degeneration …

The Rise Of The Classical Gene: A Review Of In Pursuit Of The Gene: From Darwin To Dna, Michael Dietrich

Dartmouth Scholarship

Review of The rise of the classical gene: a review of In Pursuit of the Gene: From Darwin to DNA by James Schwartz, 2008.

Comparative Vegetative Anatomy And Systematics Of Laeliinae (Orchidaceae), William Stern, Barbara Carlsward

Faculty Research & Creative Activity

Laeliinae are one of the most prominent orchid subtribes, with c. 40 genera and nearly 1500 species, and contain a disparate group of taxa with widely varying morphological features. There does not appear to be a complex of characters to which one can refer in order to delineate the subtribe as a whole. Thus, it was thought that vegetative anatomy might provide clues to the monophyly of the group. The microscopic structure of the leaves, stems and roots of representatives of most of the genera was studied. It was concluded that the anatomy lacks overall uniformity and that vegetative characters …

Comparative Vegetative Anatomy And Systematics Of Laeliinae (Orchidaceae), William Louis Stern, Barbara S. Carlsward

Faculty Research & Creative Activity

Laeliinae are one of the most prominent orchid subtribes, with c. 40 genera and nearly 1500 species, and contain a disparate group of taxa with widely varying morphological features. There does not appear to be a complex of characters to which one can refer in order to delineate the subtribe as a whole. Thus, it was thought that vegetative anatomy might provide clues to the monophyly of the group. The microscopic structure of the leaves, stems and roots of representatives of most of the genera was studied. It was concluded that the anatomy lacks overall uniformity and that vegetative characters …

Thyroid Hormone Regulation Of Mrnas Encoding Thyrotropin Β-Subunit, Glycoprotein Α-Subunit, And Thyroid Hormone Receptors Α And Β In Brain, Pituitary Gland, Liver, And Gonads Of An Adult Teleost, Pimephales Promelas, Sean C. Lema, Jon T. Dickey, Irvin R. Schultz, Penny Swanson

Biological Sciences

Thyroid hormones (THs) regulate growth, morphological development, and migratory behaviors in teleost fish, yet little is known about the transcriptional dynamics of gene targets for THs in these taxa. Here, we characterized TH regulation of mRNAs encoding thyrotropin subunits and thyroid hormone receptors (TRs) in an adult teleost fish model, the fathead minnow (Pimephales promelas). Breeding pairs of adult minnows were fed diets containing 3,5, 3^,-triiodo-_L-thyronine (T₃) or the goitrogen methimazole for 10 days. In males and females, dietary intake of exogenous T₃ elevated circulating total T₃, while methimazole …

A Comparative Ecological Study Of Two Sister Species Of Darters In Kentucky, Etheostoma Kantuckeense And Etheostoma Lawrencei, Bjorn Victor Schmidt

Masters Theses & Specialist Projects

Etheostoma kantuckeense and E. lawrencei are former members of the wide ranging E. spectabile species complex. Etheostoma kantuckeense is endemic to the Barren River Basin in Southern Kentucky and Northern Tennessee, while E. lawrencei occurs in the Green River, Salt River, and Cumberland River Basins of Central and Eastern Kentucky. Isolation of populations within these drainages has allowed for a relatively recent evolutionary divergence, leading to slight differences in morphology. This study was conducted to address if geographical isolation has led to measurable differences in the ecology of these two species. In particular, habitat preference across three spatial scales and …

The Effect Of Breeding Herd Parity Structure On Genetic Improvement Of The Sow Herd, Caitlyn E. Abell

Mahurin Honors College Capstone Experience/Thesis Projects

This study focuses on the value of the genetic lag associated with maintaining sows for additional parities in a commercial swine herd. Three traits were included in this study: number born alive (NBA), 21 day litter weight (W21), and days to market (D250). The economic values assigned to these traits were $22.00/pig, $0.70/lb., and $0.17/day, respectively. The genetic improvement per generation made for each trait was assumed to be 0.3 pigs, 3.0 lbs., and 3.0 days, respectively. It was estimated that the value of the genetic lag associated with retaining a sow to P3, P5, and P7 was $24.80, $46.89, …

Empirical Testing Of 16s Rrna Gene Pcr Primer Pairs Reveals Variance In Target Specificity And Efficacy Not Suggested By In Silico Analysis, Sergio E. Morales, William E. Holben

Biological Sciences Faculty Publications

Phylogenetic and "fingerprinting" analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primers for phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, we created a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone library containing similar to 5,000 …