Biology Commons^™

Breaking Boundaries In Computing In Undergraduate Courses, Kam D. Dahlquist, John David N. Dionisio, Ran Libeskind-Hadas, Anna E. Bargagliotti

Biology Faculty Works

An important question in undergraduate curricula is that of incorporating computing into STEM courses for majors and non-majors alike. What does it mean to teach “computing” in this context? What are some of the benefits and challenges for students and instructors in such courses? This paper contributes to this important dialog by describing three undergraduate courses that have been developed and taught at Harvey Mudd College and Loyola Marymount University. Each case study describes the course objectives, implementation challenges, and assessments.

The Rtfa Gene Regulates Plant And Animal Pathogenesis And Secondary Metabolism In Aspergillus Flavus, Jessica Michelle Lohmar

Graduate Research Theses & Dissertations

Aspergillus flavus is an opportunistic fungal plant and human pathogen and producer of mycotoxins including aflatoxin B1 (AFB1). As part of our ongoing studies to elucidate biological functions of the A. flavus rtfA gene, we examined its role in pathogenicity of both plant and animal model systems. rtfA encodes a putative RNA-Pol II transcription elongation factor, previously characterized in Saccharomycese cerevisiae, Aspergillus nidulans, Aspergillus fumigatus, where it was shown to regulate several important cellular processes, including morphogenesis, secondary metabolism. In addition, an initial study in A. flavus indicated that rtfA also influences development and production of AFB1, however its effect …

Reproductive Promiscuity In The Variegated Fairy-Wren: An Alternative Reproductive Strategy In The Absence Of Helpers?, Allison E. Johnson, Stephen Pruett-Jones

School of Biological Sciences: Faculty Publications

Cooperative breeding, in which auxiliary group members help rear related, but nondescendent young, is often explained by kin selection. Reproductive monogamy is predicted in cooperatively breeding systems, as monogamy increases intragroup relatedness and maximizes auxiliary inclusive fitness. While monogamy is observed across many systems, including eusocial insects and cooperatively breeding mammals, some cooperatively breeding birds exhibit high rates of extrapair paternity. Here we quantify paternity and examine the role of auxiliaries on extrapair paternity in the highly cooperative variegated fairy-wren, Malurus lamberti, a species with both male and female auxiliaries. Extrapair paternity occurred in 55.4% of nests, and 39.8% …

Nutrigenomics: Using Sulforaphane Consumption As A Mechanism To Prevent Cardiovascular Disease Through Epigenetic Regulation, Alisha Agrawal

UROP Posters

Cardiovascular disease is the leading cause of death in the United States. Diet composition and reduced expression of the transcription factor Nrf2 are both possible factors contributing to cardiovascular disease. As vitamin supplementation grows in scope and popularity, it is becoming common to replace vegetable consumption with multivitamins. The purpose of this research was to investigate how sulforaphane, an isothiocyanate found in its greatest quantities in broccoli, prevents cardiovascular disease through epigenetic regulation in order to promote the understanding that vitamin supplementation does not adequately replace the health benefits of phytonutrients found in vegetables. In order to investigate sulforaphane’s ability …

The Forensic Characterization Of Bacterial And Fungal Organisms In Traditional Chinese Medicine, Julia Grzymkowski, Christopher J. Ehrhardt, Justin L. Poklis, Michelle R. Peace

UROP Posters

There has been an increase in use of Traditional Chinese Medicine (TCM) in the United States because they are less expensive and believed to be more effective with less adverse effects in comparison to traditional pharmaceutics. Therefore, sales have increased in the US, despite articles and case studies demonstrating the dangers, such as injury and death, related to TCM, stemming from improper labelling, toxic contaminants, and, in some cases, the presence of pathogenic bacteria. The aim of this study was to perform a survival experiment to demonstrate the importance of proper herbal brewing technique and to conduct a molecular and …

Functional Variation In The Mitochondrial Genome Of The Yeast Saccharomyces Cerevisiae, John F. Wolters

Graduate Dissertations and Theses

Mitochondrial haplotypes contribute to functional diversity in natural populations. Uniparental inheritance makes it difficult to characterize the genetic architecture of mitochondrially driven phenotypes. In this work I explored the natural diversity of mitochondrial genomes in the yeast Saccharomyces cerevisiae. Few complete mitochondrial genomes were available for S. cerevisiae owing to challenges in high-throughput sequencing. I developed sequencing strategies using new technologies to generate complete high quality yeast mitochondrial genomes. Comparisons of 100 complete yeast mitochondrial genomes demonstrated extensive variation between populations in coding sequences and variable introns.

I demonstrated that these mitochondrial variants directly caused growth differences in strains with …

Purkinje Cell Morphology And Display Complexity In Manakins (Pipridae), Mary Harvey

Honors Theses

Manakins are a suboscine, lekking bird of the tropical and subtropical regions of South and Central America that perform complex mating displays shaped by sexual selection. The complexity of the mating display varies greatly across species of manakins. Some manakins only perform a limited number of different motor elements, whereas others have elaborate displays that consist of acrobatic movements and mechanical sound production. The complexity of these displays has been found to be positively related to brain weight, brain volume, arcopallium volume, body weight, and tarsus size but shows no relationship to the nucleus rotundus or nucleus taeniae. The volume …

Effects Of Housing Management On Vaccination Success Against Eimeria Infection In Chickens, Louis Wilson Benton

Honors Theses

Coccidiosis is a disease of the gastrointestinal system of commercially raised chickens (Gallus gallus). The infection is caused by multiple parasitic species of the coccidian genus Eimeria. Eimeria proliferate within large poultry houses leading to decreased nutrient absorption, anorexia, and death of the host. Scheduled vaccination with live coccidian oocysts should minimize production losses, but various management factors may contribute to variation in the outcome. I investigated whether by tracking infection cycles in detail it might be possible to improve poultry production. Feces were collected daily from four farms across a two-month period to understand how peaks in oocyst shedding …

Effects Of Texting On Neck Muscle Activity And Neck Flexion In College Students., Matalgah Haneen

Honors Theses

College students are susceptible to tech neck, a possible musculoskeletal disorder producing neck strain due to texting. The primary aim of this study was to determine whether texting among college students produces any significant effects on the trapezius and sternocleidomastoid muscles and neck flexion. To the best ofmy knowledge, no study in the literature has studies the effects of texting taking into consideration factors specific to college students, such as carrying a backpack and different environments (e.g. stairs, hallways). This justifies my primary aim of examining collegiate factors (i.e. backpack, environment) influence on neck muscle activity and flexion in students …

Fruit Structure In Arabidopsis Thaliana Organ Boundary Mutants, Katelyn Childers

Honors Theses

The fruit are an integral plant organ that function to nurture and disperse seeds. Â Using the model species Arabidopsis thaliana, the genetic mechanisms underlying fruit development have been carefully studied. Â The Arabidopsis fruit originates from the female reproductive organ, the gynoecium, which consists of two carpels that develop into the ovary with a style and stigma. Â Proper formation of the fruit relies on a functional floral meristem and on the specification of boundary regions that arise between the carpel walls and a medial replum. Â Two genes known to affect both the development of organ boundaries in …

The Protective Effects Of Ferrostatin-1 (Fer-1) In Response To Excitotoxicity In Mouse Hippocampal Slices, Mireya Nael Ramirez

Open Access Theses & Dissertations

The development of different neurological disorders has been associated with the accumulation of reactive oxygen species (ROS). Elevated ROS levels can disrupt the neuronal electrical activity. This phenomenon has been seen during epilepsy and neurodegenerative diseases like Parkinson's disease. Furthermore, the excess of ROS and development of such disorders have been linked to neuronal cell death partly due to excessive, non-physiological glutamate release. Ferroptosis is a recently defined iron-dependent cell death mechanism. Inducible by a small molecule called erastin, ferroptosis was first described in cancer cells. Erastin-induced ferroptosis differs from apoptosis, necrosis and autophagy, since it leads to different biochemical …

Glycoconjugate-Based Vaccines For Chagas Disease, Brenda Guadalupe Zepeda

Open Access Theses & Dissertations

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi. About 6–8 million people are estimated to be infected worldwide. It is a blood borne pathogen and transmitted to humans by the insect vector (kissing bug), blood transfusion, organ transplant, contaminated foods and juices, and by congenital contagion. The chemotherapy is partially effective in chronic phase of the disease, and the drugs cause several side effects. There is no vaccine to prevent or treat Chagas disease. The great majority of experimental vaccines have employed whole parasite extracts, purified or recombinant proteins, synthetic peptides, or DNA; however, most of them provide …

Hidden Diversity In Aquatic Habitats: Lessons From Cryptic Species In Microscopic Invertebrates (Rotifera), Azar Kordbacheh

Open Access Theses & Dissertations

Speciation is a continuous and adaptive process by which lineages are diverged into multiple groups, and species are the product of this process. Taxonomy is the study of relationship between organisms, classifying and naming them, and one of the taxonomical challenges is delimiting species boundaries. Species delimitation can be controversial because biologists do not agree on species concepts and approaches for defining species boundaries. One of the well-known species concepts is the Biological Species Concept that requires studying reproductive barriers among populations. Investigating strength of reproductive isolation among populations is not always practical in the wild. Therefore, many biologists have …

Birds And Vegetation Structure Of Isolated Juniper And Oak Communities In The Trans-Pecos Chihuahuan Desert., Kayla Garza

Open Access Theses & Dissertations

Birds of the Trans-Pecos region are historically understudied, with most literature covering birds of desert grasslands and scrub in New Mexico and Northern Mexico. A multitude of vegetation communities within the Chihuahuan Desert have also been neglected due to this gap in the research, for reasons including lack of access to public or preserve land in West Texas, and rough terrain. Indio Mountains Research Station (IMRS), is located 42-km southwest of Van Horn, Texas and encompasses many different vegetation communities, including juniper-oak habitats of arroyo and canyon systems. The purpose of this study was to document the bird species utilizing …

Functional Investigation Of A Brainstem Excitatory Connection Relevant To Sensorimotor Gating, Luis Enrique Martinetti

Open Access Theses & Dissertations

To focus attention, our brain has to "gate" or block irrelevant sensory information that could lead to brain overload. This is done by way of a neuronal pre-attentive mechanism termed sensorimotor gating (SG). Therefore, deficits in the SG mechanism prevent patients from focusing attention. SG deficits have been observed in patients suffering from various neurological disorders, and it is a hallmark of schizophrenia. Previous work has identified key brain areas, such as the pedunculopontine tegmental nucleus (PPTg), that send inputs to the brainstem to regulate SG. However, there is still a knowledge gap concerning what cell types are involved and …

The Role Of Climate In The Dynamics Of Annual Plants In A Chihuahuan Desert Ecosystem, Danielle D. Ignace, Nancy Huntly, Peter Chesson

Biology Faculty Publications

Question: What is the role of temporal climate fluctuations in the dynamics of desert winter annual plants in the Portal Bajada, and in the sustained irruption of the non-native annual plant species, Erodium cicutarium?

Field site: Portal Bajada, San Simon Valley, Arizona, USA.

Methods: We counted plants at flowering over a 21-yeaer period on twelve permanent plots and related these numbers to weather data collected at an on-site weather station, supplemented by observations from the National Climate Data Center. Specific summary climate variables considered most relevant to annual plant biology were developed as candidate predictors of plant response variables. …

Environmental Gradients In Old‐Growth Appalachian Forest Predict Fine‐Scale Distribution, Co‐Occurrence, And Density Of Woodland Salamanders, J. Alex Baecher, Stephen C. Richter

EKU Faculty and Staff Scholarship

Woodland salamanders are among the most abundant vertebrate animals in temperate deciduous forests of eastern North America. Because of their abundance, woodland salamanders are responsible for the transformation of nutrients and translocation of energy between highly disparate levels of trophic organization: detrital food webs and high‐order predators. However, the spatial extent of woodland salamanders’ role in the ecosystem is likely contingent upon the distribution of their biomass throughout the forest. We sought to determine if natural environmental gradients influence the fine‐scale distribution and density of Southern Ravine Salamanders (Plethodon richmondi) and Cumberland Plateau Salamanders (P. kentucki). …

Role Of Micrornas In Impaired Gut Permeability Following Ethanol And Burn Injury, Niya Latrice Morris

Dissertations

Every year there are nearly 500,000 reported burn injuries in the United States; half of which occur under the influence of alcohol. Clinical studies have shown that burn patients who are intoxicated at the time of injury have a worse prognosis; including increased risk of multiple organ dysfunction syndrome (MODS) and sepsis. The etiology behind these pathological consequences of ethanol and burn injury remains to be elucidated. The Gut-lymph hypothesis of MODS theorizes that trauma (e.g. ethanol and burn injury) results in a redistribution of blood flow to protect more vital organs which leads to ischemia/hypoxia (diminished oxygen delivery) in …

Cryptic Diversification Of Two Widespread Species In Madagascar, Lynika Sharlice Strozier

Master's Theses

Using phylogenetic and phylogeographic tools to uncover hidden diversity within the genus Newtonia in Madagascar

Madagascar is known for its rich biodiversity and high level of endemic species that are found nowhere else. Cryptic diversification, defined as genetically and evolutionarily distinct species that are hard to detect because they are morphologically indistinguishable from their closest relatives, has been hypothesized to occur in many groups on Madagascar. Currently it is unclear to what extent this phenomenon occurs in birds because only a few studies have been conducted. My study examined the phylogenetic and phylogeographic patterns within a songbird genus, Newtonia, that …

Mutation Identification And Functional Analysis Of Mutant Dax-1 Proteins Found In Thai Patients With X-Linked Adrenal Hypoplasia Congenita, Chanisara Suthiworachai

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mutations in the DAX-1 gene result in X-linked adrenal hypoplasia congenita (X-linked AHC), a rare congenital disorder of adrenal insufficiency with defects in adrenal gland development and steroid biosynthesis. Male patients usually develop severe adrenal insufficiency in early infancy or childhood. In some cases, hypogonadotropic hypogonadonism (HH) is presented in puberty. DAX-1 gene product, DAX-1 protein, acts as a transcriptional repressor of genes in the steroidogenic pathway by interacting with, and repressing the steroidogenic factor 1 (SF-1) protein. In contrast, the SF-1 protein transactivates the steroidogenic acute regulatory (StAR) protein that functions in the steroid biosynthetic pathway. The aim of …

Effects Of Habitat Enhancement On Bird Diversity In Kaeng Khoi District, Saraburi Province, Dijan Sunar Rukmi

Chulalongkorn University Theses and Dissertations (Chula ETD)

Various techniques of habitat enhancement have been used to increase the habitat quality, consequently enriching biodiversity and maintaining ecosystem services. This study aims to assess the effects of habitat enhancement on bird diversity, guild composition and bird usage pattern by conducting bird censuses and observations as well as arthropod samplings in the landscape-scale (LS) experiment plots and in the teak reforestation (TR) enhanced with sunflower and sunn hemp species over dry and wet seasons of 2015-2016. Sunflower treatment attracted more bird species (LS: 28, TR: 19) than sunn hemp treatment (LS: 25, TR: 15), but bird occurrence was varied based …

Taxonomy And Systematics Of Earthworm Genus Pontodrilus Perrier, 1874 In Thailand, Teerapong Seesamut

Chulalongkorn University Theses and Dissertations (Chula ETD)

A taxonomic study of the littoral earthworm genus Pontodrilus Perrier, 1874 was critically conducted based on material collected from marine sandy coasts along the east and west sides of the Thai-Malay Peninsula (Thailand and Malaysia) and selected localities in Japan. Comparative material from other parts of Southeast Asia, including Myanmar, Vietnam, Malaysia, Singapore and Indonesia, were also collected. Morphological examination identified almost all of the specimens as Pontodrilus litoralis, but as two morphotypes with some character differences in the diverticulum between them. A combined morphological and molecular phylogenetic analyses supported one of these morphotypes as a new species, P. longissimus. …

Characterization Of Two Cyclic Di-Gmp Phosphodiesterases Hypothesized To Regulate Virulence In Streptomyces Scabies, Madison Flasco

Undergraduate Honors Thesis Projects

Common scab is a devastating disease that affects the marketability of potatoes. The disease results in raised and pitted lesions seen on the surface of the potato and is caused by the soil pathogen, Streptomyces scabies. The S. scabies genome has two cyclic-di-GMP phosphodiesterases, RmdA and RmdB, both regulators of morphology and development. These proteins break down the ubiquitous second messenger molecule cyclic di-GMP, a molecule in charge of cell cycle progression and virulence. Both proteins contain diguanylate cyclase domains and phosphodiesterase domains, GGDEF and EAL, respectively, while RmdA contains an additional PAS_4 domain. Despite similar domain configurations, the two …

Effects Of Nonnative Rainbow Trout On Two Species Of Endemic Mexican Amphibians, A. B. Estrella Zamora, Geoffrey R. Smith, J. A. Lemos-Espinal, G. A. Woolrich-Pina, R. Montoya Ayala

Faculty Publications

No abstract provided.

Evaluation And Adaptation Of Live-Cell Interferometry For Applications In Basic, Translational, And Clinical Research, Kevin A. Leslie

Theses and Dissertations

Cell mass is an important indicator of cell health and status. A diverse set of techniques have been developed to precisely measure the masses of single cells, with varying degrees of technical complexity and throughput. Here, the development of a non-invasive, label-free optical technique, termed Live-Cell Interferometry (LCI), is described. Several applications are presented, including an evaluation of LCI’s utility for assessing drug response heterogeneity in patient-derived melanoma lines and the measurement of CD3+ T cell kinetics during hematopoietic stem cell transplantation. The characterization of mast cells during degranulation, the measurement of viral reactivation kinetics in Kaposi’s Sarcoma, and drug …

The Ability Of Phyllospadix Spp., A Pair Of Intertidal Foundation Species, To Maintain Biodiversity And Ameliorate Co2 Stress In Rocky Shore Tidepools, Tayler M. Tharaldson

Cal Poly Humboldt theses and projects

Ocean acidification (OA) is often demonstrated to have negative effects on marine organisms, but less is known about whether marine organisms can mediate OA effects. I examined relationships between surfgrass (Phyllospadix spp.), a foundation species and tidepool biodiversity, and its ability to mediate fluctuations in pH and dissolved oxygen (OA; DO) which are stressors in tidepools. I surveyed tidepools in northern California, where I quantified biodiversity, pH, and DO, and related those variables to surfgrass abundance. Laboratory and field experiments manipulating CO₂ and surfgrass presence were done to examine surfgrass effects on day/night pH and DO fluctuations …

The Genome Of Austrofundulus Limnaeus Offers Insights Into Extreme Vertebrate Stress Tolerance And Embryonic Development, Josiah Tad Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven Cody Woll, Jake Roush, Wesley C. Warren, Anne Brunet, Jason E. Podrabsky

Center for Life in Extreme Environments Publications

Background: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.

Results: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy …

Evolution Belief Trends, Jamie Jensen

ScholarsArchive Data

This is the essay code frequencies along with the raw survey data for both Cohort 1 and Cohort 2 for the following paper:

Bradshaw, WS, Phillips, AJ, Bybee, SM, Gill, RA, Peck, SL, Jensen, JL. 2018. A longitudinal study of attitudes toward evolution among Mormon undergraduates. PLOSONE.

Noninvasive Collection Of Saliva In Panthera Leo : Creation And Validation Of A Novel Technique For Health Assessment In Captive African Lions (Panthera Leo), Elizabeth Sgambelluri

Antioch University Dissertations & Theses

Very little research exists concerning direct correlations between alterations in stress stimuli and direct effects on carnivore physiology. Many studies have researched and documented what factors correlate to increased stress levels in predator species. Lacking, however, are studies observing the specific physiologic influences of increased glucocorticoid concentrations in those individuals. Furthermore, methods for monitoring and assessing health or immune function in many carnivore species often involve invasive techniques, such as physical restraint, blood sampling, and chemical immobilization. This study aimed to create, evaluate, and describe a new device for noninvasive collection of saliva for health assessment. The device itself was …

Influences Of Forest Edges And Human Activities On The Dry Season Ranging Patterns Of Chimpanzees (Pan Troglodytes Schweinfurthii) In Nyungwe National Park, Rwanda, Enathe Hasabwamariya

Antioch University Dissertations & Theses

Great apes, our closest biological relatives are threatened globally by the increasing anthropogenic pressures on their habitat. The major threats to the eastern chimpanzees (Pan troglodytes schweinfurthii) are hunting for bush meat and illegal trade in chimpanzee infants, habitat loss or fragmentation and disease transmission (IUCN, 2010). Nyungwe National Park (NNP), Rwanda has a population of chimpanzees that face several threats, including hunting for bushmeat, habitat degradation from forest fires and human-wildlife conflicts, and much of these impacts are concentrated at forest edges. The main objectives of this research were to assess the use of forest edges by chimpanzees along …