Life Sciences Commons^™

Fern Community Reassembly In Secondary Forests Of Puerto Rico: Predictors, Complexity, And Niche Model Assessment, Thomas J. Schmidt

Masters Theses

Approximately 94% of Puerto Rico’s forests were converted into agricultural systems by 1950. Since then, extensive abandonment of agricultural land has resulted in a considerable amount of forest regeneration throughout the main island. Ferns are a major non-woody component of oceanic, tropical island forests comprising up to seventy percent of the flora. Consequently, the composition and community structure of ferns may be indicative of the relative richness of these secondary forests. I used Maximum Entropy (Maxent), a widely-used mathematical tool for distinguishing suitable versus unsuitable fern niche space, along with ENMTools, a tool that assists Maxent with proper model selection, …

Genetic Structure Of Yellow Perch Populations In Coastal Areas Of Eastern Lake Michigan, Jessica N. Wesolek

Masters Theses

Genetic population substructure is often overlooked because of discontinuities between management and actual population structure as in the case of yellow perch, an ecologically and economically important indigenous fish species in the Laurentian Great Lakes. A knowledge gaps pertaining to the natural history of yellow perch relates to the biological connectivity between nearshore Lake Michigan and drowned river mouth (DRM) lakes, where it remains unclear whether resident yellow perch from Lake Michigan use DRM lakes for spawning or whether DRM lakes contribute to nearshore yellow perch populations in Lake Michigan. I used DNA fingerprinting (genotyping) to explore biological connectivity between …

Structural Comparison Of Arctic Plant Communities Across The Landscape And With Experimental Warming In Northern Alaska, Jessica L. Gregory

Masters Theses

Understanding vegetation change is central to forecasting the impacts of climate change. Percent cover, determined from a point frame method, is commonly used to monitor vegetation change. Cover is influenced by canopy structure which may change with the size (growth) or number (density) of individual plants. The overarching objective of this project was to document the relationship between vegetation cover and traits representing plant growth and density and determine if these relationships changed with warming. We used regressions and analysis of covariance to detect which of several traits was most strongly related to cover in vegetation at a wet and …

Characterization Of Histidine Decarboxylase In Drosophila Using An Internal Flag Epitope, Maxwell Mianecki

Masters Theses

Histamine is a neurotransmitter in arthropods and is responsible for synaptic transmission in vision, mechanosensation, temperature sensing and sleep cycle in Drosophila. Histamine is synthesized by the enzyme histidine decarboxylase (HDC). While histamine is detectable within tissues using current immunofluorescent labeling techniques, immunological approaches have not been successful for HDC itself, with both direct antibodies and terminal epitope tags determined to be ineffective. In order to avoid loss of the epitope tag through putative N-­‐ and C-­‐terminal proteolytic cleavage, known to occur for HDC in other organisms, an internal epitope tag that does not disrupt enzyme function was utilized. A …

Evaluation Of Natural Steelhead Recruitment In The Muskegon River, Michigan, Nicholas C. Albrecht

Masters Theses

The lower Muskegon River is one of the most heavily fished rivers in the state of Michigan and is a valuable component of the multi-billion dollar sport fishery in the Great Lakes. Although significant stocking effort has been invested to maintain and improve the steelhead (Oncorhynchus mykiss) fishery in the Muskegon River, natural recruitment has been severely limited due to high summer water temperatures. The goal of this research project was to evaluate the success of a diffuser system installed in 2008 at Croton Dam to moderate high summer water temperatures in the lower Muskegon River. I estimated natural juvenile …

Genetic Health And Population Viability Of Reintroduced American Marten In Michigan, Tamara L. Hillman

Masters Theses

American marten (Martes americana) were extirpated from Michigan’s Lower Peninsula (LP) in 1911, and subsequently from the Upper Peninsula (UP) in 1939 due to habitat loss and unregulated trapping. The species was later reintroduced in the UP in the mid-1950s, and to the LP in the mid-1980s. Previous research has determined the small founding sizes used in the LP reintroductions have resulted in losses of genetic diversity, while research in the UP has produced discordant results concerning the effects of the reintroduction methods on genetic health and population structure. Since past research of marten in the LP, no …

Predictive Modeling Of Floral Species Richness In Michigan Prairie Fen Communities, Nichole R. Mason

Masters Theses

Prairie fens contain high levels of floral biodiversity, including 19 state threatened or endangered plant species, and are classified as rare and vulnerable communities by the Michigan Natural Features Inventory. The objective of this thesis was to develop multiple-regression (MR) models that reliably predict total, native, and invasive floral species richness for use by conservation organizations. Floral biodiversity surveys were conducted in eight southern Michigan prairie fens during the 2012 growing season. Simple linear regressions between fen size and biodiversity were used to optimize sampling strategy and effort (i.e., number of transects and plots per transect) in surveys conducted in …

Spatio-Temporal Factors Affecting Human-Black Bear Interactions In Great Smoky Mountains National Park, Nathan Buckhout

Masters Theses

Wildlife managers use models to aid in predicting high risk areas for human and black bear (Ursus americanus) interactions (HBI). These tools help managers implement management strategies to minimize HBI. Over 3,000 incidents of HBI were compiled from management reports at Great Smoky Mountains National Park (GSMNP) during 1998-2011, a park with 9-10.2 million visitors per year and a black bear population of about 1,600 bears.

We used data from bear management reports along with annual visitor use, mast and bear abundance data to develop a series of generalized linear models to assess the spatial and temporal factors …

The Role Of The Novel Lupus Antigen, Acheron, In Moderating Life And Death Decisions, Ankur Sheel

Masters Theses

Programmed cell death (PCD) is a major regulatory mechanism employed during development and homeostasis. The term PCD was coined to describe the death of the intersegmental muscles (ISMs) of moths at the end of metamorphosis. The timing of ISM death in the Tobacco Hawkmoth, Manduca sexta, is regulated by a fall in the titer of the steroid molting hormone 20-hydroxyecdysone (20E) late on day 17of pupal-adult development. This triggers the release of the peptide hormone, Eclosion Hormone (EH), which mediates its effects via the secondary messenger cGMP. It has been previously demonstrated that ISM death requires de novo gene expression. …

Rapid Method Of Processing Sperm For Nucleic Acid Extraction In Clinical Research, Matthew K. De Gannes

Masters Theses

Background: Sperm contain highly compact nuclei, inhibiting DNA extraction using traditional techniques. Current methods extracting sperm DNA involve lengthy lysis and no means of stabilizing DNA, hindering clinical research.

Objective: We sought to optimize an efficient method of extracting high quality human sperm DNA.

Methods: Sperm from three volunteers were isolated using PureCeption. We tested 1) proteinase K with DNA/RNA Shield, 2) DTT and TCEP as reducing agents, 3) QIAshredder homogenization, and 4) stability of sperm DNA fresh (baseline) or after 4 weeks of storage at 4^OC in DNA/RNA Shield using modified Quick-gDNA MiniPrep. DNA was PCR amplified …

Resting Site Characteristics Of American Marten In The Northern Lower Peninsula Of Michigan, Robert L. Sanders

Masters Theses

American marten are usually associated with forests that are characteristically late successional, closed canopy, and diverse in structure; attributes that meet habitat requirements and provide resting site structures. Resting site structures are required habitat components that are used daily and provide protection from predation and inclement weather. I identified resting site characteristics of American marten in the Manistee National Forest in Michigan’s Lower Peninsula from May 2011 to December 2013. Twenty five marten (15 male and 10 female) were monitored using radio telemetry to identify what types of resting sites structures were used. I identified 522 unique resting site structures; …

Spatial And Temporal Variation Of Macroinvertebrate Communities In The Muskegon River And Bigelow Creek, Michigan, Travis Hauri Foster

Masters Theses

The first objective of this study was to determine the relationship between zebra mussel densities/biomass and benthic macroinvertebrate composition and density in the Muskegon River at a site near Croton Dam, Thirteen benthic quadrat samples were taken along a range of zebra mussel and macroinvertebrate densities at a single sample location. Turbellaria was the only taxa to have a significant positive relationship with zebra mussel density and biomass, Simuliidae had a positive, non-significant relationship with both. No macroinvertebrate taxa decreased because of zebra mussel density/biomasss. The other objectives of this study were to compare current macroinvertebrate communities in the Muskegon …

The Initial Effects Of Community Variables On Sand Prairie Restoration: Species Establishment And Community Responses, Robert Christopher Roos

Masters Theses

We established a sand prairie restoration experiment in northern Lower Michigan’s pine-oak barrens to analyze the effect of different community variables (vegetative cover, species richness, biomass, diversity, and floristic quality) when comparing: (1) how our restoration efforts (seeded treatments) compare to natural community succession (control plots), (2) how different seeding treatments affect these community variables, specifically when evaluating (2a) the effect of grass seeding densities; and (2b) the effect of different forb guilds (early flowering, late flowering, and legumes) during the initial two growing seasons of restoration establishment. In general, a comparison between seeded treatments and non-seeded control treatments indicates …

Genetic Analysis Of Ancient Human Remains From The Early Bronze Age Cultures Of The North Pontic Steppe Region, Jeff Pashnick

Masters Theses

During the Neolithic transition into the Early Bronze Age (EBA) in the North Pontic steppe region (NPR), people, cultures, and technologies were rapidly changing. Farming was on the decline and Indo-European languages were spreading through the region along with pastoralist way of life. In this study we used mitochondrial DNA (mtDNA) haplotyping to study the people living in the NPR during these times. Additionally, we used next-generation sequencing (NGS) technologies in attempts to develop novel methods to assess the degradation of ancient DNA (aDNA). We extracted ancient mtDNA from remains of 11 individuals belonging to late Neolithic and EBA populations …

Historical Demography And Dispersal Patterns In The Eastern Pipistrelle Bat (Perimyotis Subflavus), Alynn M. Martin

Masters Theses

The recent emergence of threats to North American bat conservation has prompted increased population genetics research on high risk species. The eastern pipistrelle bat is affected by both white-nose syndrome and wind turbine mortality. However, little work has been done regarding the population structure and effective population size of this species. Using the HVI region of the mitochondria and eight microsatellite loci, I analyzed male and female structure across the sample range of P. subflavus and estimated the effective population size of their populations. Pairwise F_ST values indicate that there is one panmictic population based on microsatellite data, while …

Wetland Sediment Nutrient Flux In Response To Proposed Hydrologic Reconnection And Climate Warming, James T. Smit

Masters Theses

Wetland restoration and creation are common practices, but wetlands restored or created on former agricultural land may act as a source of nutrients, rather than as a sink. I studied P sediment-water exchange in two flooded celery fields (west and east), which are designated for wetland restoration, in order to assess the effects that hydrologic reconnection of the area to an adjacent creek would have on P dynamics. We also examined the influence of climate change, specifically warming temperatures, by conducting the sediment-water exchange experiments at ambient and plus 2°C temperature conditions. Lab-based sediment core incubations revealed that TP release …

Population Ecology Of Northern Bobwhite (Colinus Virginianus) On A Reclaimed Surface Mine, David Cole Peters

Masters Theses

Direct linkages between habitat management and northern bobwhite (Colinus virginianus) survival are not well documented; therefore, we implemented an experiment to evaluate those responses. We conducted our experiment on a reclaimed surface mine, a novel landscape where conditions were considered sub-optimal for bobwhite. Nonetheless, these areas have great potential for contributing to bobwhite conservation. Our objectives were to determine if habitat management could improve (1) seasonal and (2) nest survival, how (3) multi-scale habitat contributed to seasonal and nest survival, and (4) conduct life stage simulation analyses (LSA) to determine which vital rates were affecting population growth rate. …

Influence Of Substrate Orientation On Feeding Kinematics Of Algae Grazing Lake Malawi Cichlid Fishes, Maxwell Friedrich Rupp

Masters Theses

Lake Malawi cichlids have been studied extensively in an effort to elucidate the mechanisms underlying their adaptive radiation. This divergence is proposed to have happened via processes such as habitat partitioning, trophic specialization, and sexual selection. However, in the rock-dwelling mbuna of Lake Malawi this divergence likely involves how and where species feed on algae within the rocky reefs they exclusively inhabit. For three species of mbuna, we quantified feeding kinematics on substrates at different orientations that mimicked the top, sides, and bottoms of the algae covered boulders these species feed from in the wild. Significant differences in kinematics were …

R-Fap: Rapid Functional Annotation Of Prokaryotes Using Taxon-Specific Pan-Genomes And 10-Mer Peptides, Jordan Matthew Utley

Masters Theses

The growing implementation of next-generation sequencing technologies presents numerous fields with the opportunity to identify bacteria in near real-time. Fields such as counter-terrorism, forensics, medicine, and even microbial ecology are positioned to benefit from such advances and implementation. However, with the ability to rapidly produce high-quality sequence data comes the need to interpret this data as quickly as it is produced. While gene prediction algorithms have kept pace, functional prediction methods have not.

To bypass the need for large-scale queries to multiple databases for each newly-sequenced genome, the project detailed herein seeks to identify the genes shared within a taxonomic …

Microglia Respond To Both Permanent And Temporary Deaferentation In The Adult Zebrafish Olfactory Bulb, Amanda K. Mckenna

Masters Theses

The major goal of this study was to investigate a microglial response following deafferentation in the adult zebrafish, Danio rerio, olfactory bulb. Microglia were identified in the olfactory bulb using the 4c4 antibody and phagocytic-dependent labeling (DiA). Microglia responded to both methods of deafferentation namely, permanent (cautery) and temporary (Triton X- 100). On one and three days following both permanent and temporary deafferentation there was a significant increase in microglia in the treated olfactory bulb. At five and seven days after permanent and temporary deafferentation there was no longer a significant difference between the treated and untreated olfactory bulbs, …

Vaccinia Virus Flll Mediated Expedition Of Tanapoxvirus Replication In Cell Culture, Yih Wen Goh

Masters Theses

Tanapoxvirus (TPV) produces large but slow-forming plaques as opposed to vaccinia virus (VACV) that forms similar large plaques but more rapidly. A number of genes were identified in VACV, inclucding FllL, A33R, A34R and A36R that contribute to the regulation of virus release and dissemination, and are particularly responsible for the induction of actin tails. Among them, TPV lacks homologs of the FllL and A36R genes. F11Lmediated inhibition of RhoA-mDia signaling was shown to enhance the microtubules dynamics and modulates the cortical actin that assisted in the release of progeny virus from infected cells. To understand the possible effects of …

Investigation Of Angiogenic Effects Of Bioactive Borate Glass Microfibers And Beads In A Rodent Model, Richard Jeffrey Watters

Masters Theses

"The primary objective of this research project was to evaluate the effects of three different compositions of bioactive glass microfibers (45S5, 13-93B3, and 13-93B3Cu) and bioactive glass beads (13-93, 13-93B3, and 13-93B3Cu) on angiogenesis in subcutaneous tissue in the SKH1 'hairless' mouse. Microvascular responses to the bioactive glass implants were investigated via three experimental approaches: noninvasive vital imaging of microvasculature in dorsal skin windows; quantitative histomorphometry of microvascular densities; and quantitative PCR measurements of mRNA expression of pro-angiogenic cytokines VEGF and FGF-2. The live imaging of dorsal skin window preparations in the hairless SKH1 showed the formation of a halo-like …

Dephosphorylation Of Iqg1 By Cdc14 Temporally Regulates Actin Ring Formation, Daniel Patrick Miller

Masters Theses

"Cytokinesis is the final step in cell division when the cell separates the cytoplasm by contracting a ring composed of filamentous actin (F-actin) and type II myosin. Iqg1, an IQGAP family member, is an essential scaffolding protein in budding yeast (S. cerevisiae) required for actin recruitment to, and contraction of, the actomyosin ring. Actin is recruited by the calponin homology domain (CHD) in anaphase after Iqg1 is localized to the bud neck. Consensus sites for the cyclin-dependent kinase (CDK) Cdc28 were identified flanking the CHD. This led us to the hypothesis that phosphorylation of Iqg1 by Cdc28 negatively regulates actin …

Ecology Of A Declining Great Plains Fish, Fundulus Sciadicus, In The Missouri Ozarks, Gregory Travis Thompson

Masters Theses

"Anthropogenic habitat disturbances are of growing concern due to their impacts on native biota, especially in freshwater ecosystems. Damming, channelization, urbanization, wetland draining, and non-native fish introductions all play large roles in habitat homogeneity, fragmentation, and species competition. This has negative effects on native fish and invertebrate species. In the Midwestern United States, the plains topminnow (Fundulus sciadicus) has been declining across its range, to the point of becoming a species of special concern in Missouri. This is possibly due to a combination of the above anthropogenic habitat disturbances. To better understand the ecology of the plains topminnow …

Characterization Of A Plant Gene Family Expanded In Glycine Max, Lisa Snoderly-Foster

Masters Theses

"Glycine max, commonly named the cultivated soybean, is one of the oldest and most important food crops in the world. The study of the G. max genome provides valuable insight into the molecular mechanisms that govern its reproduction and environmental responsiveness, key factors in maximizing crop yield. Since the complete sequencing of the genome in 2010, the analysis has become faster and easier, especially with the development of numerous web-based, publically accessible bioinformatics tools.

This research effort utilizes these tools to characterize a small, unannotated G. max gene family. Although no definitive evidence was uncovered for the production of a …

Energy Tradeoffs Between Food Assimilation, Growth, Metabolism And Maintenance, Lihong Jiao

Masters Theses

"The effect of metabolic rate (MR) on organisms' health maintenance is a long-standing puzzle and empirical data on this issue is contradictory. A theoretical model was developed for understanding animal's energy budget under the food condition of Ad libitum (AL) and food restriction. This model offers a framework for understanding the role of MR and health maintenance mechanism from the perspective of energy tradeoff between food assimilation, growth, metabolism and maintenance. Hornworm (Manduca sexta larva) has been selected as an model to test the energetic tradeoff under different food supply and ambient temperatures. The changes in energy budget can …