Biology Commons^™

Beta-Diversity Patterns And Community Assembly Across Latitudes, Emma Moran

Arts & Sciences Graduate Student Theses and Dissertations

A major goal of community ecology is in understanding variation in community composition, generally termed β-diversity. This variation can result from a variety of mechanisms, including deterministic factors, wherein species sort along biotic or abiotic gradients; stochastic processes, whereby random fluctuations in population sizes cause variation in community composition; and/or dispersal limitation. Although all of these processes are likely occurring in all biological communities, a key question in community ecology research is if their relative importance may vary systematically across environmental or biogeographic gradients. In this dissertation, we combine both observational and experimental research to investigate β-diversity across a biogeographic …

Metabolic Regulation Of Cd8 T Cell Functions In The Tumor Microenvironment, Jing Qiu

Arts & Sciences Graduate Student Theses and Dissertations

Failure of T cells to protect against cancer is thought to result from lack of antigen recognition, chronic activation, and/or suppression by other cells. Using a mouse sarcoma model, we show that glucose consumption by tumors metabolically restricts T cells in the tumor microenvironment, leading to their dampened mTOR activity, glycolytic capacity, and IFN-γ production, and thereby allowing tumor progression. We demonstrate that enhancing glycolysis in an antigenic ‘regressor’ tumor is sufficient to override the ability of T cells to respond to a major tumor rejection antigen, allowing progression of tumors that are normally rejected. Checkpoint blockade therapy is used …

The Role Of Histidine Rich Protein Ii In Cerebral Malaria, Priya Pal

Arts & Sciences Graduate Student Theses and Dissertations

Human malaria is caused by five species of Plasmodium. Of these, P. falciparum is the deadliest and is the only species that causes cerebral malaria (CM). CM is a disease of the vascular endothelium characterized by parasite sequestration, increased inflammatory cytokine production, vascular leakage and leukocyte infiltration. A distinguishing feature of P. falciparum infection is the parasite’s production and secretion of histidine-rich protein II (HRPII). HRPII accumulates to high concentrations (up to 100 µg/ml) in serum, which correlates with disease severity. Due to high serum levels of this protein, HRPII has classically been considered a biomarker for P. falciparum infection. …

The Role Of Bhlhe40 In Autoimmune Neuroinflammation And Mycobacterial Infection, Chih-Chung Lin

Arts & Sciences Graduate Student Theses and Dissertations

The mammalian immune system is composed of innate and adaptive compartments, which cooperate with each other to maintain homeostasis and protect the host from the invasion by a variety of pathogens. The tight control of immune responses is extremely important for all individuals. Here, we discovered that the transcription factor basic helix-loop-helix family, member e40 (Bhlhe40) is a critical protein that regulates the autoimmune ("against self") and anti-microbial ("against non-self") responses of myeloid cells and T lymphocytes. Multiple sclerosis (MS) is a human neuroinflammatory disease in the central nervous system with an autoimmune etiology. We have reported that Bhlhe40 positively …

Modeling Complex Patterns Of Differential Dna Methylation That Associate With Expression Change, Christopher E. Schlosberg

Arts & Sciences Graduate Student Theses and Dissertations

Gene expression is driven by specific combinations of transcription factors binding to regulatory sequences to define cell type expression profiles. Changes in DNA sequence alter transcription factor binding affinities and gene expression, and DNA methylation is an additional source of variation that is maintained throughout cellular division. Numerous genomic studies are underway to determine which genes are abnormally regulated by DNA methylation in disease. However, we have a poor understanding of how disease-specific methylation variation affects expression. Global DNA demethylation agents have been clinically approved for use in cancer, which has spurred interest in identifying genes which would be most …

Defining The Ontogeny And Functions Of Macrophages In Pancreatic Ductal Adenocarcinoma, Yu Zhu

Arts & Sciences Graduate Student Theses and Dissertations

The immune system plays an essential role in protecting the host organisms against both foreign invaders and self-attacks arisen within the host, such as tumors. Instead of promoting the long-term fitness of the organism, the immune system is often suppressed or hijacked by tumor cells to accelerate the progression of malignancies. Among the key drivers of immune suppression, macrophages are one of the most abundant immune cells present in tumor tissues. High levels of macrophage infiltration in the malignant tissues correlate with negative patient outcome in many types of cancers, including pancreatic ductal adenocarcinoma (PDAC), one of the most lethal …

Natural History And Evolution Of An Elevational Generalist, The Cinereous Conebill (Conirostrum Cinereum), Andrea N. Chavez, Chandresekhar Natarajan, Jay F. Storz, Angela Fago, Christopher C. Witt

Biology ETDs

Elevational generalism is relatively rare in the tropical Andes Mountains, likely owing to the inherent requirements of enduring a high degree of climatic zonation and coping with hypoxic stress. The Cinereous Conebill (Conirostrum cinereum) appears to be an exception, and inhabits a continuous elevational distribution that spans over 4,500 m. Two subspecies, cinereum and fraseri, are restricted to high elevations and may be isolated, whereas the third and most widespread, littorale, occurs continuously along the western slope of the Andes from 0 to over 4,500 m. First, we aim to characterize the morphology, genetics, and climatic …

Buried Alive: Urban Stream Burial In Grand Rapids, Michigan, Tanner Vincent

Student Papers and Reports

In the decades between 1913 and 1967, Silver and Coldbrook Creeks vanished from the urban landscape in the rapidly growing city of Grand Rapids, Michigan. A U.S. Geological Survey (USGS) map of Grand Rapids from 1914 shows both Silver and Coldbrook Creeks emptying into the Grand River west of their headwaters south and north of Reeds Lake, respectively. By 1967, the year a topographical map of Grand Rapids was created at a scale as fine as that of the 1914 map, both Silver and Coldbrook Creek had been erased from the landscape of Grand Rapids. A closer look at the …

The Effects Of Atmospheric Pressure On Inter-Specific Competition And The Morphological And Hematological Characteristics Of Elevational Distributions Of Hummingbirds, Ariel Marie Gaffney

Biology ETDs

Species diversity in mountainous regions is strongly influenced elevational range limits of species, but it is generally not known which abiotic or biotic factors maintain these limits. Using Black-chinned and Broad-tailed Hummingbirds, species with offset but overlapping elevational ranges in the southwestern USA, we investigate the role barometric pressure plays in influencing these limits. In chapter one, we used a hypobaric chamber to test the effects of variable air pressures on interspecific competitive dominance. We sequenced the genes that encode the two adult isoforms of haemoglobin and measured the O₂-binding affinity of each isoform. In chapter two, we …

Precipitation Patterns And Fungal Community Succession In A Seasonally Dry Secondary Tropical Savanna, Sara R. López-Rodríguez

Biology ETDs

In the northwestern part of South America, seasonally dry forests have undergone extensive conversion to savannas to support ranching and agriculture. The combination of fire and vegetation removal employed for clearing, together with extensive agricultural practices, often lead to loss of soil fertility. This results in land that is no longer useful for agriculture and on which historical forests are unable to regenerate. This study examined the effects of common agricultural practices on soil fungal communities by simulating the effects of fire followed by plant removal. The goal was to determine whether common practices have rapid effects on soil communities, …

Immunology Of The Gray Short-Tailed Opossum During Pregnancy And Prenatal Development, Victoria L. Hansen

Biology ETDs

Vertebrate species that bear live young have overcome the evolutionary challenge of maintaining both a functional adaptive immune system and viviparous life cycle. In normal pregnancy, viviparous mothers are able sustain and nourish a fetus that is genetically half non-self without mounting an immunological attack. In 1953 Sir Peter Medawar brought attention to the “enigma of the fetal graft” and immunologists have been puzzling out the intricacies of fetal tolerance ever since. Although viviparity has evolved in all jawed vertebrate lineages aside from Aves, the vast majority of reproductive immunology research has been limited to eutherian mammals. There are insights …

Bio Buzz Newsletter, Issue 13, May 2017, Department Of Biology

Biology Buzz Newsletter

Denison University, Department of Biology newsletter for Spring 2017.

Spatial Structure Of The Mormon Cricket Gut Microbiome And Its Predicted Contribution To Nutrition And Immune Function, Chad C. Smith, Robert Srygley, Frank G. Healy, Karthikeyan Swaminath, Ulrich G. Mueller

Biology Faculty Research

The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the niches available for microbes to colonize. We present a high-resolution analysis of the structure of the gut microbiome in the Mormon cricket Anabrus simplex, an insect known for its periodic outbreaks in the western United States and nutrition-dependent mating system. The Mormon cricket microbiome was dominated by eleven taxa from the Lactobacillaceae, Enterobacteriaceae, and Streptococcaeae. While most of …

A Comparative Study Of Microbial Community Of Undisturbed And Reclaimed Soil In Southeast Kansas, Ghaidaa Allhyani

Electronic Theses & Dissertations

The purpose of this project is to compare the microbial communities of the 33 year-old soil at the Monahan with the original soil at the O'Malley. The data collected in this project investigates whether there is a correlation between soil age and the soil microbial community. Using soil DNA analysis is one way we can compare soil microbial communities. Soil DNA was isolated from multiple samples from both sites using DNA isolation kit. Using the community DNA as a template, eubacterial, archaeal, and fungal DNA fragments were PCR amplified using specific-primers. The amplicons were purified and are being processed for …

Bacterial Diversity At An Abandoned Coal Mine In Southeast Kansas, Rachel Bechtold

Electronic Theses & Dissertations

Bacterial Diversity at an Abandoned Coal Mine in

Southeast Kansas

An Abstract of the Thesis by

Rachel Bechtold

Acid mine drainage (AMD) is found in areas of abandoned coal mines in southeast Kansas as a result of mine waste rocks and tailings create problems for the local environment. Soil bacterial population acts as a reliable indicator of ecosystem health in these human-perturbed areas. The goals of the present study were to assess the bacterial diversity of an AMD site over a two-year period and to isolate acid-tolerant bacterial species for bioremediation purpose.

In fall (2015) and summer (2016), soil samples …

Identification Of The Potentiating Mutations And Synergistic Epistasis That Enabled The Evolution Of Inter-Species Cooperation, Sarah Douglas, Lon Chubiz, William Harcombe, Christopher Marx

Biology Department Faculty Works

Microbes often engage in cooperation through releasing biosynthetic compounds required by other species to grow. Given that production of costly biosynthetic metabolites is generally subjected to multiple layers of negative feedback, single mutations may frequently be insufficient to generate cooperative phenotypes. Synergistic epistatic interactions between multiple coordinated changes may thus often underlie the evolution of cooperation through overproduction of metabolites. To test the importance of synergistic mutations in cooperation we used an engineered bacterial consortium of an Escherichia coli methionine auxotroph and Salmonella enterica. S. enterica relies on carbon by-products from E. coli if lactose is the only carbon source. …

Draft Genome Sequences Of 25 Listeria Monocytogenes Isolates Associated With Human Clinical Listeriosis In Ireland, Eamonn P. Culligan, Et. Al.

Department of Biological Sciences Publications

Listeria monocytogenes is a Gram-positive opportunistic pathogen that is the causative agent of listeriosis. Here, we report the draft genome sequences of 25 L. monocytogenes strains isolated from patients with clinical listeriosis in the Republic of Ireland between 2013 and 2015.

Marine Tardigrades From South Carolina, Usa, Paul J. Bartels, Lilvia J. Bradbury, Diane R. Nelson

Journal of the South Carolina Academy of Science

Until now, there have been only three studies of marine tardigrades from South Carolina, USA. The Fall 2015 invertebrate zoology class from Warren Wilson College collected four sediment samples from Huntington Beach State Park: shallow beach sand, deep beach sand, shallow salt marsh sediment, and deep salt marsh sediment. No tardigrades were found in the salt marsh, but two species were found in the beach samples. Batillipes pennaki Marcus, 1946 was found in shallow and deep beach sand, and three specimens of a potentially new species of Stygarctus Schulz, 1951 were found in the deep beach sand at groundwater level. …

Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan

DEEPEND Datasets

The deep sea ecosystem is believed to contain the highest biomass of fish in the oceans. However, the taxonomic diversity in this ecosystem is incompletely described and likely to be vastly underestimated. DNA sequence data (barcodes) have become a key tool to discover hidden biodiversity. We generated mitochondrial DNA barcode datasets based on the Cytochrome c oxidase I (COI) gene from deep sea fishes. These data were analyzed using phylogenetic and statistical methods to reveal cryptic species and make taxonomic linkages between adult fishes and their early life stages. These datasets were generated from fishes collected in the Northern Gulf …

Application Of Anthromes To Frame Scenario Planning For Landscape-Scale Conservation Decision Making, Dainee Gibson, John Quinn

Biology Publications

Complexities in the rates and patterns of change necessitate the consideration of alternate futures in planning processes. These scenarios, and the inputs and assumptions used to build them, should reflect both ecological and social contexts. Considering the regional landscape as an anthrome, a priori, assumes human needs and institutions have a fundamental role and place in these futures, but that institutions incorporate ecological limits in decision making. As a case study of conservation scenario planning under the anthrome paradigm, we used a suite of InVEST models to develop and explore land use and land cover scenarios and to measure the …

Horizontally Acquired Biosynthesis Genes Boost Coxiella Burnetii's Physiology, Abraham S. Moses, Jess A. Millar, Matteo Bonazzi, Paul A. Beare, Rahul Raghavan

Biology Faculty Publications and Presentations

Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C. burnetii are different from that of Coxiella-like bacteria found in ticks. Horizontally acquired genes that …

Effects Of Carrion Decomposition On Arthropod Community Structure And Habitat Seeking Behavior, Samantha J. Sawyer

Honors Program Theses and Projects

No abstract provided.

High Fructose Corn Syrup Down-Regulates The Glycolysis Pathway In Apis Mellifera, Michelle R. Jennette

Honors Program Theses and Projects

Over the past few years, honeybee populations (Apis mellifera) have drastically decreased due to Colony Collapse Disorder (CCD). CCD occurs when most of the honeybees abandon their hive and queen, and do not return. Around the same time CCD became commonly identified, commercial beekeepers switched the bee’s food from sucrose to a less expensive, but more processed substitute of high fructose corn syrup (HFCS), suggesting there might be a relationship between the types of food and CCD. Therefore, the goal of this project is to identify changes in carbohydrate metabolism due to HFCS. To determine these changes, gene …

Jaz Levels In Arabidopsis After Infection By Parasitic Root-Knot Nematode, Ashley Smith

Honors Program Theses and Projects

Root-knot nematodes (Meloidogyne spp.) are a major problem in the United States; damaging millions of dollars’ worth of crops every year. It is believed that root-knot nematodes (RKN) alter the expression of JAZ gene family members in the plant, Arabidopsis thaliana, but there is not much documentation on which genes change expression and why. The JAZ genes are transcriptional regulators in the signaling pathway for the plant hormone, Jasmonic acid, which controls certain aspects of plant defense. There are twelve JAZ genes in Arabidopsis but it is unclear if they each have distinct roles in Jasmonic acid …

The Effects Of A High Fat Diet And Lithium On Social And Anxiety-Like Behaviors In Bipolar And Autistic Mouse Strains, Nicole L. Arruda

Honors Program Theses and Projects

Bipolar Disorder (BD), or manic-depressive illness, is a psychiatric disease in which an individual experiences sudden changes in mood, activity, and overall energy. Individuals with the disorder switch between excessive joy and excitement, and extremely sad and hopeless episodes. A common treatment of BD is lithium, a mood stabilizer that helps to relieve manic symptoms. Lithium has been known to contribute to the onset of diabetic-like symptoms, in addition to a large correlation, up to three times higher risk, of developing Type II Diabetes in individuals with BD. In general, individuals who consume a high fat diet (HF) are often …

Effects Of Habitat Fragmentation On The Population Genetics Of Plethodon Cinereus, Matthew Tucker

Honors Program Theses and Projects

Genetic diversity is important to the long-term survival of a species. Populations with low genetic diversity are more likely to go extinct due to an inability to adapt to environmental changes or accumulation of deleterious alleles. Habitat fragmentation may result in lower genetic diversity by disrupting gene flow between subpopulations caused by urbanization and development (e.g., roads, buildings, and agricultural fields). This study explored the effects of habitat fragmentation on the genetic diversity of the eastern red-back salamander (Plethodon cinereus). I collected tissue samples from 20-30 individuals from 1-3 different subpopulations within four larger forest sites that differed …

Effectiveness Of Cattail (Typha Spp.) Management Techniques Depends On Exogenous Nitrogen Inputs, Kenneth J. Elgersma, Jason P. Martina, Deborah E. Goldberg, William S. Currie

Faculty Work

Wetlands occupy a position in the landscape that makes them vulnerable to the effects of current land use and the legacies of past land use. Many wetlands in agricultural regions like the North American Midwest are strongly affected by elevated nutrient inputs as well as high rates of invasion by the hybrid cattail Typha × glauca. These two stressors also exacerbate each other: increased nutrients increase invasion success, and invasions increase nutrient retention and nutrient loads in the wetland. This interaction could create a positive feedback that would inhibit efforts to manage and control invasions, but little is known …

Altered Na, K- Atpase Isoform Expression In Artemia Franciscana In Response To Hypersaline Environments, Jessica Drenth

Theses and Dissertations

The Na,K-ATPase (NKA) is an essential membrane pump that helps to establish cell ion gradients, and regulate intracellular salt in many organisms. One such species, Artemia franciscana (brine shrimp), extreme halophiles which live in hypersaline environments, expresses 2 distinct α-catalytic subunits of the NKA. One of these subunits, α2-(KK), has two key lysine substitutions located within the cation binding sites. Prior work has demonstrated this specific subunit may be directly involved in brine shrimp adaptation to their extreme environments. However, the precise molecular and physiological effects of α2-(KK) have not been entirely elucidated. I determined through immunohistochemistry that my initial …

Rat Hind Limb Nociceptive Withdrawal Response To Heat And Mechanical Stimuli Depends On Initial Position Of The Paw But Not Stimulus Location, Giavanna Verdi

Senior Honors Projects, 2010-2019

Mammals rapidly withdraw their hind limb in response to noxious stimulation, which is a protective movement known as the nociceptive withdrawal response (NWR). The NWR has been previously studied in spinalized, decerebrated and anesthetized non-human and human mammals; however, there is minimal information on the NWR in intact, unanesthetized non-human mammals.

The first specific aim was to identify the factors that determine the direction and magnitude of the NWR in intact, unanesthetized rats. Based on previous studies, we hypothesized that the location of stimulation and the initial position of the paw preceding the NWR will influence the direction and magnitude …

Searching For Sex Differences In Snake Skin, Sydney E. Ashton

Senior Honors Projects, 2010-2019

The production of many secondary sexual signals, including pheromones, is controlled by sex hormone action at the sites of signal synthesis. The red-garter snake (Thamnophis sirtalis parietalis) is an ideal vertebrate for studying the interaction between steroids and sexual signals: males exclusively rely on skin-based female pheromones during courtship, and pheromone composition is augmented by treatment with sex steroids (e.g., males produce female pheromone if implanted with estrogen). But how do steroid hormones promote pheromone expression at the molecular level in snake skin? Feminizing effects of estrogens on sexual signals are known to result from activation of estrogen …