Biology Commons^™

Dj-1 And Atp13a2: Two Proteins Involved In Parkinson’S Disease, Josephat M Asiago

Open Access Dissertations

Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, affecting approximately 0.3% of the total U.S. population, and its prevalence increases with age. Two neuropathological hallmarks of PD are the loss of dopaminergic neurons in the substantia nigra pars compacta, a region in the midbrain involved in initiating and sustaining movement, and the presence of cytosolic inclusions called Lewy bodies (LBs) in various brain regions. LBs are enriched with fibrillar forms of the presynaptic protein &agr;-synuclein (aSyn). Two autosomal recessive genes implicated in familial PD are PARK9, encoding the P-type ATPase ATP13A2, a lysosomal ATPase; and …

The Effects Of Phragmites Australis Litter On Seed Emergence In The Erie-Huron Corridor, Michigan, Travis White

Wayne State University Theses

The invasive reed, Phragmites australis, is widespread within the Great Lakes region, and is often blamed for habitat degradation. Once established, it creates dense litter mats that may persist following remediation efforts of living stock removal. We investigated the effects of P. australis and Typha angustifolia, narrow-leaf cattail, litter on seedling emergence from the native seed bank by harvesting soils from five Great Lakes coastal marshes densely populated by either Phragmites or Typha and exposing them to Phramities or Typha litter in treatments of varying litter depths. Seedling emergences were quantified for six weeks. Soils from Phragmites dominated sites had …

Effects Of Extreme Hydrologic Events On Trout Populations And Fish Communities In A Catskill Mountain River, Scott Daniel George

Legacy Theses & Dissertations (2009 - 2024)

Extreme hydrologic events are becoming more common with changing climatic conditions. Although the impacts of winter and spring floods on lotic ecosystems have been well studied, the effects of summer floods on fish assemblages in mountain streams are less well known. This study took advantage of an extreme precipitation event during the course of an ongoing monitoring program, which allowed the opportunity to quantify the effects of a severe late summer flood on fish communities in a montane watershed. We also evaluated the effect of the flood on the density and age structure of two ecologically important populations of sport …

Refining Aquatic Macroinvertebrate Community Metrics For The Assessment Of Headwater Streams In New York State, Brian T. Duffy

Legacy Theses & Dissertations (2009 - 2024)

The River Continuum Concept describes the structural and functional shift that occurs from sensitive headwater streams to the lowest reaches of large, non-wadeable rivers. New York State (NYS) maintains a long-established biological monitoring program using macroinvertebrate community assemblages for water quality assessment. However, headwater streams are rarely assessed, and no reference models are available, except those calibrated for lower-continuum wadeable streams and rivers. Current patterns of rural landuse change emphasize the need for more accurate assessment of previously neglected headwaters, in order to set natural reference standards for more accurate assessments of water quality. Ecoregion, drainage area (DA), elevation (elev.), …

The Effects That Liquid And Solid Cattle Manure Have On The Water Quality Of Drainage Ditches In Putnam County, Ohio, Janelle Horstman

Honors Projects

Lake Erie has experienced harmful algal blooms with increased frequency since the mid-1990s due to excess nutrients from Rivers, such as the Maumee River, and largely agricultural watersheds. Nonpoint source pollution from agriculture contributes to eutrophication, algal blooms, and the degradation of water quality. This creates stress on aquatic fauna, reduced aesthetic quality, odor, and limits of the water for usage of drinking, recreation, and industry. This research paper asks what the contributions of having access to manure application records, soil records, and information about antibiotics have on what is known about manure management and antibiotic resistance, which has been …

Synthesis And Characterization Of Brain Penetrant Prodrug Of Neuroprotective D264: Potential Disease Modifying Treatment Agent For Parkinson's Disease, Fahd Shamoon Dholkawala

Wayne State University Theses

Parkinson's disease (PD) is a complex neurodegenerative disorder with progressive loss of dopamanergic neurons in the substantia nigra region of the brain and accumulation of intracytoplasmic inclusions called `Lewy bodies'. PD is characterized by tremors, rigidity, slowness of movement, bradykinesia and postural imbalances. Although the etiology of PD is not well understood, it is well established that oxidative stress, mitochondrial dysfunction, alpha-synuclein aggregation play a central role in the pathogenesis of PD. Current treatment methods are based on symptomatic relief without addressing the underlying pathophysiological factors responsible for the disease. It is important to develop therapies which can address these …

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 …

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 …

Art Or Science?, Allison Marsh

Section 3: Imaging the Fast Moving

No abstract provided.

Position Of Premature Termination Codons Determines Susceptibility Of Herg Mutations To Nonsense-Mediated Mrna Decay In Long Qt Syndrome, Qiuming Gong, Matthew R. Stump, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

The degradation of human ether-a-go-go-related gene (hERG, KCNH2) transcripts containing premature termination codon (PTC)mutations by nonsense-mediatedmRNA decay (NMD) is an importantmechanismof long QT syndrome type 2 (LQT2). The mechanisms governing the recognition of PTC-containing hERG transcripts asNMD substrates have not been established. We used a minigene system to study two frameshift mutations, R1032Gfs*25 and D1037Rfs*82. R1032Gfs*25 introduces a PTC in exon 14, whereas D1037Rfs*82 causes a PTC in the last exon (exon 15). We showed that R1032Gfs*25, but not D1037Rfs*82, reduced the level of mutant mRNA compared to thewild-type minigene in an NMD-dependent manner. The deletion of intron 14 prevented …

Biomechanical Effects Of Trees And Soil Thickness In The Cumberland Plateau, Michael Shouse

Theses and Dissertations--Geography

Previous research in the Ouachita Mountains, Arkansas suggests that, on relatively thin soils overlying bedrock, individual trees locally thicken the regolith by root penetration into bedrock. However, that work was conducted mainly in areas of strongly dipping and contorted rock, where joints and bedding planes susceptible to root penetration are more common and accessible. This project extended this concept to the Cumberland Plateau, Kentucky, with flat, level-bedded sedimentary rocks. Spatial variability of soil thickness was quantified at three nested spatial scales, and statistical relationships with other potential influences of thickness were examined. In addition, soil depth beneath trees was compared …

Winter Survival Strategies Of Benthic Invertebrates In Temporary Habitats In A Northern Minnesota Lake, Cal Oldenburg

Journal of Earth and Life Science

During the winter months in the northern hemisphere, above 40 degrees latitude, a freezing event occurs that can last several months. Some lakes may have large portions of the shallow littoral zone frozen completely solid down into the sediments. Invertebrates affected by these events have developed survival strategies to cope with the harsh environment. The two main strategies for invertebrates in these areas are to either migrate to a different area and recolonize the original area when it becomes available again, or to burrow into the sediments and withstand the freezing. A 1- month study took place on Lake Bemidji …

Genetic Variation, Local Adaptation And Population Structure In North American Red Oak Species, Quercus Rubra L. And Q. Ellipsoidalis E. J. Hill, Jennifer F. Lind-Riehl

Dissertations, Master's Theses and Master's Reports - Open

Forest trees, like oaks, rely on high levels of genetic variation to adapt to varying environmental conditions. Thus, genetic variation and its distribution are important for the long-term survival and adaptability of oak populations. Climate change is projected to lead to increased drought and fire events as well as a northward migration of tree species, including oaks. Additionally, decline in oak regeneration has become increasingly concerning since it may lead to decreased gene flow and increased inbreeding levels. This will in turn lead to lowered levels of genetic diversity, negatively affecting the growth and survival of populations. At the same …

Effects Of Toxic Cyanobacteria (Microcystis Aeruginosa) On The Feeding And Reproduction Ecology Of The Copepod Eurytemora Affinis From Green Bay, Lake Michigan, Nicholas J. Barrett

Lawrence University Honors Projects

Toxic Cyanobacteria is known to be a bad food source to consumers as well as a main contributor to harmful algal blooms. This study investigates the feeding relationship between an invasive copepod in the Great Lakes system, Eurytemora affinis, and a toxic strain of cyanobacteria, Microcystis aeruginosa. E.affinis has been shown to feed on toxic cyanobacteria. By measuring the filtering rate, ingestion rate, egg production and offspring size between three different food conditions, we hope to gain insight into the effects of toxic cyanobacteria on the feeding and reproduction of this copepod. Food sources include a good green algal …

Modular Network Construction Using Eqtl Data: An Analysis Of Computational Costs And Benefits, Yen Yi Ho, Leslie M. Cope, Giovanni Parmigiani

Faculty Publications

Background: In this paper, we consider analytic methods for the integrated analysis of genomic DNA variation and mRNA expression (also named as eQTL data), to discover genetic networks that are associated with a complex trait of interest. Our focus is the systematic evaluation of the trade-off between network size and network search efficiency in the construction of these networks. Results: We developed a modular approach to network construction, building from smaller networks to larger ones, thereby reducing the search space while including more variables in the analysis. The goal is achieving a lower computational cost while maintaining high confidence in …

Remediation Of Tetracycline From Water Sources Using Vetiver Grass (Chrysopogon Zizanioides L. Nash) And Tetracycline-Tolerant Root-Associated Bacteria, Aparupa Sengupta

Dissertations, Master's Theses and Master's Reports - Open

Antibiotics are emerging contaminants worldwide. Due to insufficient policy regulations, public awareness, and the constant exposure of the environment to antibiotic sources has created a major environmental concern. Wastewater treatment plants (WWTP) are not equipped to filter-out these compounds before the discharge of the disinfected effluent into water sources (e.g., lakes and streams) and current available technologies are not equipped to remediate these compounds from environmental sources. Hence, the challenge remains to establish a biological system to remove these antibiotics from wastewater. An invitro hydroponic remediation system was developed using vetiver grass (Chrysopogon zizanioides L. Nash) to remediate tetracycline …

Denitrification In Soils: From Genes To Environmental Outcomes, Jianqiu Zheng

Dissertations, Master's Theses and Master's Reports - Open

Denitrification is an important process of global nitrogen cycle as it removes reactive nitrogen from the biosphere, and acts as the primary source of nitrous oxide (N₂O). This thesis seeks to gain better understanding of the biogeochemistry of denitrification by investigating the process from four different aspects: genetic basis, enzymatic kinetics, environmental interactions, and environmental consequences. Laboratory and field experiments were combined with modeling efforts to unravel the complexity of denitrification process under microbiological and environmental controls.

Dynamics of denitrification products observed in laboratory experiments revealed an important role of constitutive denitrification enzymes, whose presence were further confirmed …

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 …

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 …

Patterns Of Maximum Body Size Evolution In Cenozoic Land Mammals: Eco-Evolutionary Processes And Abiotic Forcing, Juha J. Saarinen, Alison G. Boyer, James H. Brown, Daniel P. Costa, S.K. Morgan Ernest, Alistair R. Evans, Mikael Fortelius, John L. Gittleman, Marcus J. Hamilton, Larisa E, Harding, Kari Lintulaakso, S. Kathleen Lyons, Jordan G. Okie, Richard M. Sibly, Patrick R. Stephens, Jessica Theodor, Mark D. Uhen, Felisa A. Smith

School of Biological Sciences: Faculty Publications

There is accumulating evidence that macroevolutionary patterns of mammal evolution during the Cenozoic follow similar trajectories on different continents. This would suggest that such patterns are strongly determined by global abiotic factors, such as climate, or by basic eco-evolutionary processes such as filling of niches by specialization. The similarity of pattern would be expected to extend to the history of individual clades. Here, we investigate the temporal distribution of maximum size observed within individual orders globally and on separate continents. While the maximum size of individual orders of large land mammals show differences and comprise several families, the times at …

Two-Photon Microscopy For Biomedical Studies, Yassel Acosta

Open Access Theses & Dissertations

Fluorescence optical microscopy is one of the most important tools to investigate biological samples and to observe structures in living cells. Based on the principle of the simultaneous absorption of two-photons and subsequent emission of fluorescent light we have developed a Two-Photon Laser Scanning Fluorescence Microscope that allow us to perform optical sectioning and three-dimensional reconstructions of structures in biological samples such as dopaminergic clusters of neurons and tracheal branches in Drosophila brain. The spatial confinement of the excitation light to the focal plane combined with the temporal compression of photons into short packets during femtosecond pulses make our system …

Spingolipid Metabolism In A Reptillian Protozoan, Entamoeba Invadens, Duran Dogan Debons

Open Access Theses & Dissertations

Entamoeba invadens (hereinafter E. invadens) is an anaerobic parasitic protozoan that can be found in water and soil. Although the host organisms for this parasite are snakes, lizards, and other reptile species, the parasite is morphologically identical to Entamoeba histolytica, a causative agent of human amebiasis. Entamoeba inavdens exists in two morphological forms--(1) a replicative trophozoite, and (2) a relatively dormant cyst. While the transformation of cyst to trophozoites (called "excystation") takes place in the stomach, the differentiation of trophozoites to cyst (known as "encystation"), occurs in the small intestine. Unlike the cyst, a trophozoite is unable to survive …

"Mining" For A Reference Condition In Southern West Virginia Streams, Matthew Rouch

Theses and Dissertations

Quarterly samples were used to estimate assemblage-level (all species combined) fish production within three minimally-impacted, southern West Virginia streams. The total annual fish production estimate was highest in Slaunch Fork (37.52 kg∙ha^-1∙y^-1), a tributary of the Tug Fork River, and lowest in Cabin Creek (10.59 kg∙ha^-1∙y^-1), a Guyandotte River tributary. Creek Chub Semotilus atromaculatus, Mottled Sculpin Cottus bairdii and Blacknose Dace Rhinicthys atratulus were the most abundant species among sites, accounting for >90% of all sampled individuals. Reference condition criteria were also selected and metrics calculated for each of the three …

Reproductive Phase Determination In Male Meagre (Argyrosomus Regius, Sciaenidae): Testis Development And Histologic Corroboration Of A Gross Anatomical Scale, Nuno Prista, Leonel Gordo, José Lino Costa, Maria José Costa, Cynthia Jones

OES Faculty Publications

Reproductive stage determination of male gonads has received sparse attention in fish biology literature with few studies detailing the building of gross anatomical- and histologic scales. The meagre (Argyrosomus regius) is one of the world's largest sciaenids and supports a significant regional fishery in European and North African waters whose reproductive patterns are yet to be fully investigated. In the present study, we derive a macroscopic grading system for meagre testis using semi-quantitative graphs that feature the testis variability along the species size range and time of the year. We then describe the histological stages and reproductive phases of male …

Modelling Cholera In Periodic Environments, Drew Posny, Jin Wang

Mathematics & Statistics Faculty Publications

We propose a deterministic compartmental model for cholera dynamics in periodic environments. The model incorporates seasonal variation into a general formulation for the incidence (or, force of infection) and the pathogen concentration. The basic reproduction number of the periodic model is derived, based on which a careful analysis is conducted on the epidemic and endemic dynamics of cholera. Several specific examples are presented to demonstrate this general model, and numerical simulation results are used to validate the analytical prediction.

Epistasis In Predator-Prey Relationships, Iuliia Inozemtseva

College of Graduate Studies: Theses & Dissertations

Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator- prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.

Closing The Knowing-Doing Gap In Invasive Plant Management: Accessibility And Interdisciplinarity Of Scientific Research, Virginia Matzek, Justin Covino, Jennifer L. Funk, Martin Saunders

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Like many conservation disciplines, invasion biology may suffer from a knowing-doing gap, where scientific research fails to inform management actions. We surveyed California resource managers to evaluate engagement with scientific research and to identify research priorities. We examined managers' access to information, judgment of the usefulness of existing research, ability to generate scientific information, and priorities for future research. We found that practitioners rely on their own experience, and largely do not read the peer-reviewed literature, which they regard as only moderately useful. Less than half of managers who do research carry out experiments conforming to the norms of hypothesis …

Effects Of Salinity And Dissolved Organic Matter On Cu Toxicity To Americamysis Bahia In Estuarine Environments, Rabia Nasir

Theses and Dissertations (Comprehensive)

As salinity increases the geochemical speciation of Cu is altered as a result of organic/inorganic complexation/competition. Such salinity changes may further challenge the osmoregulatory capabilities of euryhaline organisms. This chemical-biological interaction complicates the understanding of the impacts of Cu in estuarine waters. Dissolved organic matter (DOM) has been widely established to be an important modifier of Cu toxicity in freshwaters however its effectiveness in modulating Cu toxicity across the range of salinities that occur in estuarine conditions has not been studied in a systematic manner. Site to site differences in DOM quality with respect to the potential for toxicity mitigation …

Table Of Contents, Michele Harmon

Journal of the South Carolina Academy of Science

No abstract provided.

Dose Dependent Effects Of Caffeine On Cognitive Performance And Neuronal Activation, Stephan Albrecht, Helen Morris, Michelle Vieyra

Journal of the South Carolina Academy of Science

Many students assume that the more caffeine you drink, the better your cognitive performance. Over-consumption of caffeine has many negative effects, so if there are no dose related cognitive benefits to large amounts of caffeine, then college students should limit their intake. This study looked at whether ingesting a medium dose (200 mg) versus a lower dose (100 mg) of caffeine improved short term memory as measured by Flanker and n-back tests, compared to a control group. In addition, we looked at whether larger doses of caffeine produced a difference in neuronal activation during these tests as measured by functional …