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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 …

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 …

Chromatin-Modifying Agents Convert Fibroblasts To Oct4+ And Vegfr-2+ Capillary Tube-Forming Cells, Anita Wary, Neil Wary '18, Jugajyoti Baruah, Victoria Mastej, Kishore K. Wary

Student Publications & Research

Rationale
The human epigenome is plastic. The goal of this study was to address if fibroblast cells can be epigenetically modified to promote neovessel formation.

Methods and results
Here, we used highly abundant human adult dermal fibroblast cells (hADFCs) that were treated with the chromatin-modifying agents 5-aza-2'-deoxycytidine and trichostatin A, and subsequently subjected to differentiation by activating Wnt signaling. Our results show that these epigenetically modified hADFCs increasingly expressed β-catenin, pluripotency factor octamer-binding transcription factor-4 (OCT4, also known as POU5F1), and endothelial cell (EC) marker called vascular endothelial growth factor receptor-2 (VEGFR-2, also known as Fetal Liver Kinase-1). In microscopic …

Vegetative Rapid Assessment And Habitat Quality Analysis Of Steidtmann Woods, Sarah Mae Bail

Honors Projects

Due to invasive species and the assumption of an unhealthy ecosystem, Steidtmann Woods is an underutilized piece of land owned by Bowling Green State University. However, the property had never been analyzed. The proposed hypothesis was that Steidtmann was indeed in destress and its ecosystem could benefit from intervention—removal of invasive species and supplementation of natives. Through a rapid vegetative analysis, data was collected in several regions of the woods to identify what navies and non-natives were present as well as to identify their proportions. With that data, the species evenness, richness, and diversity was calculated; first, with raw field …

Where The Wild Things Are: Investigating Body Size As A Mechanism For Persistence, Meghan Anne Balk

Biology ETDs

Body size is a trait under selection. Genetic drift, climate, diet quality, and biotic interactions all select upon body size at the population, species, and community levels. These factors can be important in the context of rapidly changing climate. One of the ways an animal can persist in its environment is through morphological adaptation in situ. Here, I investigate four questions relating to the evolution of body size: (1) what is the limit in body size change in response to climatic change; (2) how does body size influence the thermal tolerances of animals; (3) how does body size evolve …

Trap-Neuter-Return Programs And The Importance Of Associated Public Awareness, Nicolette Sliwa

Biology: Student Scholarship & Creative Works

The focus of this paper is to describe a typical Trap-Neuter-Return (TNR) program and highlight the major pros and cons surrounding this somewhat controversial method of managing the overwhelming free-roaming cat population. The effects of the species’ overabundance on the environment and human health are also discussed. Citing studies completed on TNR programs around the globe as well as mathematical models, the effectiveness of this method is compared to other, currently used alternatives. Finally, it has been suggested that the general awareness level a neighborhood possesses about the true goals of TNR programs has a potentially significant impact on the …

Mitochondria Mediate Cell Membrane Repair And Contribute To Duchenne Muscular Dystrophy., Maria C Vila, Sree Rayavarapu, Marshall W Hogarth, Jack H Van Der Meulen, Adam Horn, Aurelia Defour, Shin'ichi Takeda, Kristy J. Brown, Yetrib Hathout, Kanneboyina Nagaraju, Jyoti K. Jaiswal

Genomics and Precision Medicine Faculty Publications

Dystrophin deficiency is the genetic basis for Duchenne muscular dystrophy (DMD), but the cellular basis of progressive myofiber death in DMD is not fully understood. Using two dystrophin-deficient mdx mouse models, we find that the mitochondrial dysfunction is among the earliest cellular deficits of mdx muscles. Mitochondria in dystrophic myofibers also respond poorly to sarcolemmal injury. These mitochondrial deficits reduce the ability of dystrophic muscle cell membranes to repair and are associated with a compensatory increase in dysferlin-mediated membrane repair proteins. Dysferlin deficit in mdx mice further compromises myofiber cell membrane repair and enhances the muscle pathology at an asymptomatic …

Hepatocellular Cancer Genome And Transcriptome Analysis Validates Clinically Significant Mutational Signatures With The Tgf-𝛃 Pathway, Shuyun Rao, Jian Chen, Kazufumi Ohshiro, Shoujun Gu, Sobia Zaidi, Wilma S. Jogunoori, Jon White, Nagarajan Pattabiraman, Raja Mazumder, Anelia Horvath, Ray-Chang Wu, Shulin Li, Chuxia Deng, Bibhuti Mishra, Rehan Akbanni, The Tcga Cancer Network, Lopa Mishra

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

An Amphipathic Trans-Acting Phosphorothioate Rna Element Delivers An Uncharged Phosphorodiamidate Morpholino Sequence In Mdx Mouse Myotube, H. Jain, J. Boehler, D. Verthelyi, Kanneboyina Nagaraju, S. Beaucage

Genomics and Precision Medicine Faculty Publications

An efficient method for the delivery of uncharged polyA-tailed phosphorodiamidate morpholino sequences (PMO) in mammalian cells consists of employing a synthetic 8-mer amphipathic trans-acting poly-2′-O-methyluridylic thiophosphate triester element (2′-OMeUtaPS) as a transfection reagent. Unlike the dTtaPS DNA-based element, this RNA element is potent at delivering polyA-tailed PMO sequences to HeLa pLuc 705 cells or to myotube muscle cells. However, much like dTtaPS, the 2′-OMeUtaPS-mediated internalization of PMO sequences occurs through an energy-dependent mechanism; macropinocytosis appears to be the predominant endocytic pathway used for cellular uptake. The transfected PMO sequences induce alternate splicing of either the pre-mRNA encoding luciferase in HeLa …

Human Ipsc-Derived Cerebellar Neurons From A Patient With Ataxia-Telangiectasia Reveal Disrupted Gene Regulatory Networks, Sam Nayler, Joseph Powell, Darya Vanichkina, Othmar Korn, Christine Wells, Ryan J. Taft, +Several Additional Authors

Genomics and Precision Medicine Faculty Publications

Ataxia-telangiectasia (A-T) is a rare genetic disorder caused by loss of function of the ataxia-telangiectasia-mutated kinase and is characterized by a predisposition to cancer, pulmonary disease, immune deficiency and progressive degeneration of the cerebellum. As animal models do not faithfully recapitulate the neurological aspects, it remains unclear whether cerebellar degeneration is a neurodevelopmental or neurodegenerative phenotype. To address the necessity for a human model, we first assessed a previously published protocol for the ability to generate cerebellar neuronal cells, finding it gave rise to a population of precursors highly enriched for markers of the early hindbrain such as EN1 and …

Effect Of Endurance Exercise On Micrornas In Myositis Skeletal Muscle-A Randomized Controlled Study., Jessica F Boehler, Marshall W Hogarth, Matthew D Barberio, James S Novak, Svetlana Ghimbovschi, Kristy J Brown, Li Alemo Munters, Ingela Loell, Yi-Wen Chen, Heather Gordish-Dressman, Helene Alexanderson, Ingrid E Lundberg, Kanneboyina Nagaraju

Genomics and Precision Medicine Faculty Publications

Objective

To identify changes in skeletal muscle microRNA expression after endurance exercise and associate the identified microRNAs with mRNA and protein expression to disease-specific pathways in polymyositis (PM) and dermatomyositis (DM) patients.

Methods

Following a parallel clinical trial design, patients with probable PM or DM, exercising less than once a week, and on stable medication for at least one month were randomized into two groups at Karolinska University Hospital: a 12-week endurance exercise group (n = 12) or a non-exercised control group (n = 11). Using an Affymetrix microarray, microRNA expression was determined in paired muscle biopsies taken before and …

Molecular Signatures Of Differential Responses To Exercise Trainings During Rehabilitation., Yi-Wen Chen, Chris Gregory, Fan Ye, Naoe Harafuji, Donovan Lott, San-Huei Lai, Sunita Mathur, Mark Scarborough, Parker Gibbs, Celine Baligand, Krista Vandenborne

Genomics and Precision Medicine Faculty Publications

The loss and recovery of muscle mass and function following injury and during rehabilitation varies among individuals. While recent expression profiling studies have illustrated transcriptomic responses to muscle disuse and remodeling, how these changes contribute to the physiological responses are not clear. In this study, we quantified the effects of immobilization and subsequent rehabilitation training on muscle size and identified molecular pathways associated with muscle responsiveness in an orthopaedic patient cohort study. The injured leg of 16 individuals with ankle injury was immobilized for a minimum of 4 weeks, followed by a 6-week rehabilitation program. The maximal cross-sectional area (CSA) …

Neural Circuitry For Target Selection And Action Selection In Animal Behavior, Daizaburo Shizuka, Eileen Hebets, Kim L. Hoke

Papers in Behavior in Biological Sciences

Animal behaviorists have long strived for a comprehensive understanding of the proximate and ultimate causes of complex behavior, and we propose that recent advances in neurobiology can help reshape or clarify this behavior-oriented understanding. We begin with an overview of current views of neural circuit mechanisms that mediate target selection and action selection. In target selection, different stimuli compete for priority in sensory-motor process- ing. Action selection is the process by which multiple possible motor actions compete for priority in a manner which balances the needs of the animal with opportunities or threats in the environment. We next discuss spatial …

Changing Measurements Or Changing Movements? Sampling Scale And Movement Model Identifiability Across Generations Of Biologging Technology, Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips, Sadie J. Ryan

Integrative Biology Faculty and Staff Publications

Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new and old data can be compared to test whether a behavior has changed over time. We used simulated data to assess the ability to quantify and correctly identify patterns of seabird flight lengths under observational regimes used in successive generations of wet/dry logging technology. Care must be taken when comparing data collected …

Genetic And Epigenetic Variation In Spartina Alterniflora Following The Deepwater Horizon Oil Spill, Marta Robertson, Aaron Schrey, Ashley Shayter, Christina J. Moss, Christina Richards

Integrative Biology Faculty and Staff Publications

Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation …

Microbe Biogeography Tracks Water Masses In A Dynamic Oceanic Frontal System, Anni Djurhuus, Philipp H. Boersch-Supan, Svein-Ole Mikalse, Alex D. Rogers

Integrative Biology Faculty and Staff Publications

Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living …

Suitability Of Laurentian Great Lakes For Invasive Species Based On Global Species Distribution Models And Local Habitat, Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng, John M. Drake

Integrative Biology Faculty and Staff Publications

Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model assumptions of data stationarity. Second, predicting potential range of freshwater aquatic species is complicated by the reliance on terrestrial climate measurements to develop occurrence relationships …

Accuracy Of Climate-Based Forecasts Of Pathogen Spread, Annakate M. Schatz, Andrew M. Kramer, John M. Drake

Integrative Biology Faculty and Staff Publications

Species distribution models (SDMs) are a tool for predicting the eventual geographical range of an emerging pathogen. Most SDMs, however, rely on an assumption of equilibrium with the environment, which an emerging pathogen, by definition, has not reached. To determine if some SDM approaches work better than others for modelling the spread of emerging, non-equilibrium pathogens, we studied time-sensitive predictive performance of SDMs for Batrachochytrium dendrobatidis, a devastating infectious fungus of amphibians, using multiple methods trained on time-incremented subsets of the available data. We split our data into timeline-based training and testing sets, and evaluated models on each set …

The Role Of The Y-Chromosome In The Evolution Of Autosomally Coded Traits, Ian Kutch

Electronic Theses and Dissertations

Recent work indicates that the Y-chromosome of the fruit fly Drosophila melanogaster can influence gene regulation on the autosomes and X chromosome. This newly discovered function of the Y has the potential to dramatically shape the regulatory evolution of numerous genes that reside throughout the genome; even for genes that code for both male and female traits. Given that the mechanism underlying the Y-linked influence on gene expression in D. melanogaster appears to exist in other independently evolved heterogametic sex chromosomes, the evolutionary implications of Y-linked regulatory variation (YRV) deserves to be explored. These implications include the potential for Y-chromosomes …

Measuring Bacterial Growth Using A 3d-Printable Spectrometer, Samuel R. Bunting

Williams Honors College, Honors Research Projects

Visible light spectroscopy is a commonly used technique for measuring the growth of bacterial cultures, and growth curves provide broadly important data. However, the equipment and resources required for these experiments has been restricted to higher education and industry due to high cost and sophistication. We have previously reported on an inexpensive, 3D-printable photospectrometer called the SpecPhone. This device utilizes an iPhone as the camera, along with several other, inexpensive additions to make a fully functional spectrometer. Here, the application of the SpecPhone is expanded to the quantification of actively dividing E. coli cultures. Two protocols have been developed; one …