Biology Commons^™

Mitochondrial Genome Evolution In Pupillid Land Snails, Jason D. Marquardt

Biology ETDs

Pupillid land snails (Family Pupillidae) are small (< 6mm) snails with a broad geographic distribution and often found in very high density in their habitat. The sequencing of the mitochondrial genome (mt genome) of three pupillid taxa has been undertaken to understand their genome evolution more fully. The Gastrocopta cristata mitochondrial genome is 14,060 bp in length and contains 13 protein coding genes, 2 rRNA genes and 22 tRNA genes. The Pupilla muscorum, and Vertigo pusilla genomes contain all of the same genes but are of differing total sizes, 14,149 bp and 14,078 bp respectively. The AT content of the three genomes is similar at ~71% A+T which is comparable to their closest sequenced relatives. There are no major gene rearrangements among the mt genomes of the three pupillids, but the positions of many tRNA genes differ from those of Albinaria caerulea. There is a genomic sequence region of high concentration of thymine on the leading strand of the mt genome that is shared among all three genomes as well as their relatives.

Systematics Of Longhorned Beetles (Insecta: Coleoptera: Cerambycidae), Eugenio Hernán Nearns

Biology ETDs

The longhorned wood boring beetles (Insecta: Coleoptera: Cerambycidae) are a diverse and economically important group of insects. With an estimated 4,000 genera and more than 35,000 described species, the Cerambycidae comprise one of the largest beetle families. Cerambycid beetles are found on all continents except Antarctica, from sea level to montane sites as high as 4000 m. Cerambycids are among the most serious wood boring pest species globally, affecting many agricultural crops, ornamental trees, and lumber products, causing millions of dollars in damage each year. Despite their economic importance and biological diversity, relatively little is known of cerambycid beetle ecology, …

Diversification And Coexistence In The Madagascar Olive (Noronhia, Oleaceae), Cynthia Hong-Wa

Dissertations

The long-isolated island of Madagascar provides a suitable setting for studying species diversification, with most groups of organisms there both radiating and showing a high level of endemism. Noronhia is one of these groups and represents the most successful radiation of the olive family (Oleaceae) in Madagascar, with ca. 80 species. In this study, using plastid and nuclear DNA sequences obtained from a comprehensive sampling both within Noronhia and the family, I show that Noronhia, together with Indian Ocean species of Chionanthus, form a monophyletic clade sister to African Chionanthus. The diversification of Noronhia followed a likely Cenozoic dispersal from …

Role Of Ubiquitin E3 Ligase Breast Cancer Associated Gene 2 (Bca2) In Sumoylation, Fareea Khaliq

Honors College Theses

As the occurrence of breast cancer increases around the world, the need for new therapeutic medicine becomes more vital to sustain the population. In order to accomplish this, specific mechanisms need to be understood to gain a perspective on the overall process of breast cancer development. One mechanism that is being researched is SUMOylation. The SUMOylation reaction uses small ubiquitin-like modifier (SUMO) proteins, which act as a type of post-translational modification that is necessary in order to preserve protein homeostasis and regulate cellular processes including apoptosis, cell proliferation, and response to stress. The SUMOs attach to a target protein through …

Susceptibility Of Caribbean Reef Fishes To Parasitism By Gnathiid Isopods, Ann Marie Coile

Student Theses and Dissertations

This study was conducted at shallow reef sites within Great Lameshur Bay, St. John, United States Virgin Islands during the late spring and summer of 2010 and 2011. Susceptibility to infestation by a gnathiid isopod (Gnathia marleyi: Crustacea: Isopoda) was examined among 16 species from 9 families and 3 orders of common Caribbean reef fishes. All species were susceptible to infestation by gnathiids; however, nocturnal species from the families Haemulidae and Lutjanidae had the highest infestations. In a follow up study, female gnathiids were reared to adulthood to test for differences in components of reproductive success (brood size, larval length) …

Characterization Of The Placenta-Specific 8.1 Gene Function During Zebrafish Embryogenesis, Haiting Ma

All Theses and Dissertations (ETDs)

The PLAC8 gene encodes for a small, cysteine-rich protein conserved in vertebrates that is a member of a large family of PLAC8-motif containing proteins with diverse functions in animals, plants, and algae. Recently, high levels of PLAC8 expression have been detected in aggressive colorectal cancer and invasive breast cancer, and potentially contributing to the cancer pathogenesis. However, the molecular and cellular functions of PLAC8 in vertebrate development, homeostasis, and disease remain unclear. To determine the function of PLAC8 under disease and normal conditions, in this thesis work, I identified plac8.1 as a PLAC8 homolog in zebrafish, a vertebrate model system …

The Role Of Camk-Ii In Skeletal Muscle Function And Swimming Behavior In Zebrafish, Minh Nguyen

Theses and Dissertations

Previous research showed mutations in muscle sarcoplasmic reticulum-bound calcium handler proteins cause swimming defects in embryonic zebrafish. CaMK-II is a highly conserved Ca2+/calmodulin-dependent protein kinase expressed in all vertebrates has been defined to activate and inactivate multiple Ca2+ handler proteins involved in excitation- contraction coupling and relaxation of cardiac and skeletal muscle. In this study, evidence is provided through pharmacological and genetic intervention that CaMK-II inhibition and overexpression causes swimming defects, particularly response to stimuli and swimming ability, reinforced by immunolocalization of skeletal muscle. Transient CaMK-II inactivation does not have any long-term defects to swimming behavior. Overexpression of wild-type, constitutively …

Metagenomic Analyses Of The Human Gut Virome, Alejandro Reyes

All Theses and Dissertations (ETDs)

The human gut harbors tens of trillions of microbes belonging to all three domains of life, Bacteria, Archaea, and Eukarya; most are members of Bacteria. These organisms collaborate and compete for functional niches and physical space: habitats), together forming a continuously functioning metabolic organ that influences many aspects of host biology. The factors that drive the assembly, determine the stability, and shape the adaptive responses of the gut microbiota to a variety of perturbations are the subject of intense study as greater appreciation is gained of the importance of this microbial community for human health. My thesis focused on the …

Method For Instant Saccharomyces Cerevisiae Kill Of Samples, Melissa Kohner, Sara Dick

Symposium on Research and Creative Expression (SORCE)

It is essential when studying the circadian rhythm in cells to be able to effectively stop them in time. In this experiment, we tested what would be the most successful killing agent on Saccharomyces cerevisiae. Six different agents were tested at different concentrations and amounts. After the S. cerevisiae was added to the test tube containing the agent, it was streaked on a plate after 5 and 10 minutes. The plates were incubated and then checked for growth. Ethanol was the most efficient killing agent. After an effective killing agent is determined, it can be used in further experiments measuring …

The Effects Of Tarp Wrapping On Blow Fly Oviposition During Decomposition Of Pigs, Natasha Lobosky, Jordan Stein

Symposium on Research and Creative Expression (SORCE)

The effects of blow fly oviposition on 12 young, recently deceased pigs were studied during a one month period in the fall semester of 2012. This project follows similar techniques that Dr. Bugajski used during her research project at Purdue. Using tarp-wrapped bodies as the sole variable, bare pigs were held as the control. The data that were collected included the presence or absence of larvae or adult flies, daily temperatures, samples of both larvae and adult flies, and the start and end of maggot migration. The samples of larvae and adult flies were later identified in the lab and …

Diversity And Abundance Of Aquatic Macroinvertebrates Associated With Different Benthic Substrates In The East Branch Of The Little Calumet River, Halina Hopkins, Ali Olson

Symposium on Research and Creative Expression (SORCE)

As part of an ongoing study of the effect of removing logjams to open the East Branch of the Little Calumet River for recreational purposes, we worked with park staff at the Indiana Dunes National Lakeshore on a study of the abundance and diversity of aquatic macroinvertebrates. We used a quantitative sampling technique to obtain samples of macroinvertebrates from five substrates in reaches of the river above and below four focal logjams. Diversity as measured by the Shannon-Weiner index varied with river substrate (sand=1.467, root wad=1.854, wood=1.64). Sand had the lowest average number of macroinvertebrates (92, as compared to 191 …

The Physiological And Morphological Responses Of The Bladder Urothelium To Differential Injury, Kristina Marie Stemler

All Theses and Dissertations (ETDs)

The bladder is the site of various diseases such as urinary tract infections: UTI), bladder pain syndrome/interstitial cystitis: BPS/IC), and bladder cancer. UTIs and BPS/IC primarily afflict women and treatment costs over $5 billion and almost $200 million respectively in 2006. Quality of life in BPS/IC patients is low; comparable to individuals with end stage renal disease. Recent research has identified a role for the epithelial lining of the bladder, which is usually targeted by these afflictions, in potentially contributing to enhancing pain. The bladder epithelium also showcases a rapid ability to regenerate after injury.

Knowledge of the contribution of …

The Effect Of Burning On Seed Germination And Seedling Growth Rates Of Sullivant’S Milkweed (Asclepias Sullivantii) And Common Milkweed (Asclepias Syriaca), Mary Nafziger, Given Harper, Faculty Advisor

John Wesley Powell Student Research Conference

Sullivant’s milkweed (Asclepias sullivantii) (SM) and Common milkweed (Asclepias syriaca)(CM) are native Illinois plants that are often used in prairie restoration efforts. Before the seeds can be planted using traditional mechanical planters, the filamentous coma (i.e., silk-like ballooning material) must first be physically removed from each seed, which requires hours of tedious manual labor. A more expedient way to remove the comas is to burn them. However, the impacts of burning on seed germination and seedling growth rates are unknown, which was the purpose of my study. Germination rates from unburned CM seeds (0%) were significantly …

Isolation And Characterization Of Novel Mycobacteriophages From The Central Illinois Region, Rachel Aron, Blake Beehler, Rachel Ende, Logan Garthe, Netherland Joiner, Tess Kelley, Lauren Killough, Michal Kozdronkiewicz, Jessica Kraut, Jennifer Lang, Matthew Piotrowiak, Prartana Ramachandran, Loni Walker, Faculty Advisor

John Wesley Powell Student Research Conference

Members of the Illinois Wesleyan General Biology Science Education Alliance (SEA) laboratory isolated and characterized fifteen distinctive phages capable of infecting Mycobacterium smegmatis. Each student collected soil samples from the central Illinois area and used direct plating or enrichment techniques to isolate phages. Streak assays were used to purify single phage populations. Individual phage populations were then characterized and DNA was isolated. Based on the following characteristics; plaque morphology (size and turbidity), life style (temperate or lytic) and DNA restriction patterns, we determined that each student has isolated a unique phage. The DNA from a single Mycobacteriophage, Kazan, was …

A New Species Of Frog Of The Genus Pristimantis (Strabomantidae) From A Cloud Forest In Southern Peru, Anton Baltuska, Edgar Lehr, Faculty Advisor

John Wesley Powell Student Research Conference

Frogs of the genus Pristimantis are found throughout northern South America in various habitats ranging from lowland rainforest, cloud forest and up to 4000 m in the puna. Members of the family Strabomantidae breed terrestrially without a free swimming tadpole; instead froglets hatch from terrestrially deposited eggs. Of the 455 known species of Pristimantis 123 are known from Peru. Here we describe a new species from the Cordillera Central in the Andes of southern Peru. The new species is known from only one female specimen. It is readily distinguished from all other members of the genus by a combination of …

Groves '11 Receives National Research Fellowship, Kim Hill

News and Events (Discontinued Series)

No abstract provided.

The Effects Of Selected Drugs On The Memory Recall Of Sleep Deprived Mice, Jenn Pauldurai

Capstone Research Projects

Humans often make use of the neurotransmission altering effects of drugs such as caffeine, ephedrine, and ethanol. These drugs induce changes in memory and learning ability, specifically when used for sleep deprivation. English white mice (Mus musculus) have been shown to exhibit similar cognitive changes when administered drugs while sleep deprived. A sample of 20 mice was divided into three experimental groups (each group receiving a different drug) and one control group. Maze-testing demonstrated that mice performance decreased with sleep deprivation (Treatment-1) but all groups returned to baseline performance when injected (IP) with selected drugs (Treatment-2), regardless of …

Clinical And Molecular Models Of Glioblastoma Multiforme Survival, R. Piccolo Stephen, J. Frey Lewis

Faculty Publications

Glioblastoma multiforme (GBM), a highly aggressive form of brain cancer, results in a median survival of 12–15 months. For decades, researchers have explored the effects of clinical and molecular factors on this disease and have identified several candidate prognostic markers. In this study, we evaluated the use of multivariate classification models for differentiating between subsets of patients who survive a relatively long or short time. Data for this study came from The Cancer Genome Atlas (TCGA), a public repository containing clinical, treatment, histological and biomolecular variables for hundreds of patients. We applied variable-selection and classification algorithms in a cross-validated design …

Conservation Status And Habitat Preference Of The Longhead Darter (Percina Macrocephala) (Cope) In Kinniconick Creek, Lewis County, Kentucky, Joshua Schiering

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science in Biology by Joshua Schiering on April 15, 2013.

The Extracellular Polysaccharide Pel Makes The Attachment Of P. Aeruginosa To Surfaces Symmetric And Short-Ranged, Benjamin J. Cooley, Travis W. Thatcher, Sara M. Hashmi, Guillaume L'Her, Daniel A. Hurwitz, Daniele Provenzano, Ahmed Touhami, Vernita D. Gordon

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

Biofilms are surface-mounted, multicellular communities of microbes. Biofilms are often associated with chronic infections that resist treatment, evade the immune system, and damage host tissue. An essential characteristic of the biofilm state is that constituent organisms are bound in a polymeric matrix. This matrix gives the system spatial structure and clusters bacteria near each other, facilitating intercellular interactions. The Pseudomonas aeruginosa strain PAO1 is widely studied as a model biofilm-forming organism. The polymeric matrix of PAO1 biofilms is dominated by two bacteria-produced extracellular polymers, Pel and Psl. We use a combination of optical and atomic force microscopy to examine the …

Interactive Effects Of Nitrogen And Phosphorus On Soil Microbial Communities In A Tropical Forest, Lei Liu, Tao Zhang, Frank S. Gilliam, Per Gundersen, Wei Zhang, Hao Chen, Jiangming Mo

Biological Sciences Faculty Research

Elevated nitrogen (N) deposition in humid tropical regions may exacerbate phosphorus (P) deficiency in forests on highly weathered soils. However, it is not clear how P availability affects soil microbes and soil carbon (C), or how P processes interact with N deposition in tropical forests. We examined the effects of N and P additions on soil microbes and soil C pools in a N-saturated old-growth tropical forest in southern China to test the hypotheses that (1) N and P addition will have opposing effects on soil microbial biomass and activity, (2) N and P addition will alter the composition of …

Edges And Overlaps In Northwest Atlantic Phylogeography, Safra Altman, John D. Robinson, James M. Pringle, James E. Byers, John P. Wares

Publications and Research

As marine environments change, the greatest ecological shifts—including resource usage and species interactions—are likely to take place in or near regions of biogeographic and phylogeographic transition. However, our understanding of where these transitional regions exist depends on the defining criteria. Here we evaluate phylogeographic transitions using a bootstrapping procedure that allows us to focus on either the strongest genetic transitions between a pair of contiguous populations, versus evaluation of transitions inclusive of the entire overlap between two intraspecific genetic lineages. We compiled data for the Atlantic coast of the United States, and evaluate taxa with short- and long-dispersing larval phases …

Steered Molecular Dynamics Simulations Of A Type Iv Pilus Probe Initial Stages Of A Force-Induced Conformational Transition, Joseph L. Baker, Nicolas Biais, Florence Tama

Publications and Research

Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P) from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and …

Identify Novel Mutants Defective In Bract Suppression, Dr. Clinton Whipple

Journal of Undergraduate Research

Progress has been achieved in most of the five research objectives. In some cases we have modified our original aims in the light of what can be reasonably expected of inexperienced undergraduates. Details of each aim follow:

Co-Amplification Of Mitochondrial Pseudogenes, Dr. Michael Whiting

Journal of Undergraduate Research

Funding was received from the BYU ORCA mentorship program during 2011 to support undergraduates performing research in my lab, under the mentorship of postdoctoral researchers, graduate students, and myself. During 2011, this funding provided direct support for 6 undergraduates who are in various stages of completing research projects. The following report focuses on undergraduate achievements, but also provides summary data for graduate students and other lab participants.

Combining Demographic And Life History Data To Test The Reproductive Value Hypothesis In Livebearing Fishes, Dr. Mark Belk

Journal of Undergraduate Research

The proposal was to conduct a large-scale mark-recapture project on a livebearing fish in Utah lake to evaluate size and sex-specific mortality rates of this population. The experiment was begun in mid- summer by marking over 1000 individual mosquitofish. All fish were returned to the lake alive after marking. In the original design we would recapture fish at two later intervals – late summer and early spring. At the late summer recapture time we recaptured individuals over a four day period with an intensive effort involving several undergraduates and graduate students. We recaptured only one marked individual out of the …

Byu Students Identify Genetic Factors That Modulate Cerebrospinal Fluid Protein Levels And Influence Risk For Alzheimer’S Disease, Dr. John Kauwe

Journal of Undergraduate Research

Successful enrollment in and completion of graduate programs requires a constellation of skills. Students must be prepared to plan and execute experiments, present their findings both verbally and in manuscript form and interact effectively with senior scientists in the field of their choice. In this Mentoring Environment Grant (MEG) I will mentor four undergraduate students, (David Patty, Matthew Bailey, *Iulianna Sambur and Mo Lee) as they develop skills in study design, data analysis, manuscript preparation, presentation and networking while identifying genetic factors that modulate protein levels and influence Alzheimer’s disease.

Using Cooperative Learning Groups To Research Speciation In Central American Fishes: Integrating Field Work, Molecular Phylogeography, And Video-Playback Behavior Assays, Dr. Jerry Johnson

Journal of Undergraduate Research

This mentoring environment grant was awarded in 2010 and was intended to spent over a two year period. The purpose of the project was to provide up to six students with an opportunity to participate in three different research aspects of a single research problem related to understanding speciation. Here I report on the outcomes of this project, specifically addressing the five points requested by the ORCA for MEG final reports.

Amphibians And Reptiles As Model Systems: Phylogenetic Research For Undergraduates, Dr. Jack Sites

Journal of Undergraduate Research

This award provided $20,000 to support of molecular phylogenetic work on a number of projects, including those related to my long-term focus on the “deep history” relationships of squamate reptiles (lizards and snakes), and the second more recent emphasis on phylogeographic (“shallow history”) studies of frogs and lizards. This second focus is in large measure a direct consequence of the NSF-PIRE project housed here at BYU (“Speciation in Patagonia: Establishing Sustainable International Collaborations in Evolution, Ecology, and Conservation Biology”; www.patagonia.byu.edu). In this project we focus on comparative phylogeography of selected co-distributed species in Patagonia. My lab is in charge of …

Achieving The Triple Bottom Line In The Face Of Inherent Trade-Offs Among Social Equity, Economic Return, And Conservation, Benjamin S. Halpern, Carissa J. Klein, Christopher J. Brown, Maria Beger, Hedley S. Grantham, Sangeeta Mangubhai, Mary Ruckelshaus, Vivitskaia J. Tulloch, Matt Watts, Crow White, Hough P. Possingham

Biological Sciences

Triple–bottom-line outcomes from resource management and conservation, where conservation goals and equity in social outcomes are maximized while overall costs are minimized, remain a highly sought-after ideal. However, despite widespread recognition of the importance that equitable distribution of benefits or costs across society can play in conservation success, little formal theory exists for how to explicitly incorporate equity into conservation planning and prioritization. Here, we develop that theory and implement it for three very different case studies in California (United States), Raja Ampat (Indonesia), and the wider Coral Triangle region (Southeast Asia). We show that equity tends to trade off …