Laboratory and Basic Science Research Commons^™

Evaluation Of Select Publicly Available In Silico Methods For Predicting Functional Effects Of Missense Mutations In The Galns Gene, Kathryn Davidson

Dissertations, Masters Theses, Capstones, and Culminating Projects

The ability to sequence patient DNA has led to an explosion in the reports of mutations for a number of diseases. Frequently, published reports include in silico predictions of the probability that the mutations are disease-associated. The question asked here is how well these in silico methods predict the effects of new mutations, i.e., mutations not included in the dataset(s) used for training and testing the in silico method. To address this question, we examined mutations associated, or potentially associated, with Morquio A (MPS IVA), a rare, autosomal recessive lysosomal storage disorder (LSD) caused by a deficiency of lysosomal enzyme …

Consequences Of Endogenous Mitochondrial Oxidative Stress In The Heart, Kristin Alisha Koenig

Dissertations, Masters Theses, Capstones, and Culminating Projects

For many years, it has been proposed that oxidative stress within the mitochondria causes mutations to the mitochondrial genome, resulting in changes in copy number per single cell. Ultimately, this compensatory increase in mtDNA, coupled with an increase in mutations, has been suggested to play a major role in the pathobiology of aging. However, evidence for this phenomenon is somewhat controversial. Importantly, oxidative stress can vary between individual cells; therefore, the overall goal of this project is to determine if oxidative stress causes both an altered copy number for mtDNA in singlecardiomyocytes and develop a methodology for sequencing mtDNA from …

Alendronate Alters Single Cell Gene Expression Of Cortical Osteoblast Lineage Cells During Bone Loss, Ryan Jakob Murphy

Dissertations, Masters Theses, Capstones, and Culminating Projects

The mineralized matrix of bone makes it difficult to examine specific populations of cells which are integral to the tissue using traditional molecular methods. For this study we examined single cell cortical osteoblasts derived from the femurs of C57BL/6J mice. After isolating single cells from bone, we were able to individually analyze their gene expression profiles using the quantitative polymerase chain reaction (qPCR). The mice used for the study were divided into 4 treatment groups, including ovariectomized mice (OVX) and sham surgical controls (SHAM), treated with or without the anti-resorptive bisphosphonate drug Alendronate, an effective FDA approved therapeutic for slowing …

Application Of High-Performance Liquid-Chromatography Mass-Spectrometry Platform To Study Metabolism And Epigenetic Control Of Metabolism, Kylie Patricia Mitchell

Dissertations, Masters Theses, Capstones, and Culminating Projects

Naturally occurring small molecules (metabolites, signaling intermediates) are a critical component of the information flow in biology, along with DNA, RNA, and proteins. Metabolomics is an analytical approach that seeks to comprehensively analyze naturally occurring small molecules and quantify their dynamic changes in biological systems. In recent years metabolomics has begun to provide understanding of the metabolic basis of different diseases, such as heart disease, cancer, and diabetes. Our lab built a High-Performance Liquid-Chromatography Mass-Spectrometry (HPLC-MS) based metabolomics platform to analyze metabolites from mammalian cells, spent cellular media, and model organisms such as C. elegans. We used C. elegans to …

Gain-Of-Function Mouse Models To Investigate Biological Roles Of Prmt6, Alessandra Di Lorenzo

Dissertations and Theses (Open Access)

Gain-of-function Mouse Models to Investigate Biological Roles of PRMT6

Alessandra Di Lorenzo, Ph.D. Candidate

Mentor: Dr. Mark T. Bedford

Protein Arginine Methyltransferase 6 (PRMT6) is the histone tail writer that methylates the H3R2 (arginine 2 of histone H3) residue, which counteracts the activating H3K4me3 mark. PRMT6 has been shown to behave both as transcriptional co-repressor (i.e. trhrombospondin-1, p21, p53), and co-activator (nuclear receptors). The co-repressor function of PRMT6 is likely the result of H3K4me3 antagonism, while the mechanism by which PRMT6 exerts its co-activator function has yet to be elucidated. PRMT6 is over-expressed in several types of tumors including small …

Walk-Training Increases Expression Of Gdnf In Pectoralis Muscle But Not Diaphragm From Mouse, Erin Donovan

Honors Theses

Neurotrophic factors are proteins that play an important role in the development and maintenance of neurons. Recent studies have shown that neurotrophic factors may hold promise for treating damage to the nervous system caused by trauma or diseases, such as amyotrophic lateral sclerosis or Parkinson’s disease. Glial cell line-derived neurotrophic factor (GDNF) is expressed in skeletal muscles and affects peripheral motor neurons. Results of previous studies have demonstrated that exercise can increase GDNF content in skeletal muscle of rat. The goal of the current study was to examine whether expression of GDNF in skeletal muscle of mouse is also regulated …

Analysis Of The Regulation And Function Of Cip2a To Identify Candidate Biomarkers For Prostate Cancer, Diana Savoly

Graduate School of Biomedical Sciences Theses and Dissertations

Protein Phosphatase 2A (PP2A) is a tumor suppressor involved in the regulation of several signaling pathways and the cell cycle. PP2A becomes inactivated by several inhibitors, including Cancerous Inhibitor of PP2A (CIP2A). CIP2A has been identified as an oncogene, which is over-expressed in cancers and inhibits PP2A through direct interaction. CIP2A is recognized as a biomarker for cancer; however, it is not cancer-specific. Therefore, we identified and examined the use of CIP2A-regulated proteins as potential biomarkers in prostate cancer to better diagnose prostate cancer in patients. Currently, Prostate Specific Antigen (PSA) is widely used to detect prostate cancer; however, it …

Moving Beyond The Welfare Standard Of Psychological Well-Being For Nonhuman Primates: The Case Of Chimpanzees, John P. Gluck

Experimentation Collection

Since 1985, the US Animal Welfare Act and Public Health Service policy have required that researchers using nonhuman primates in biomedical and behavioral research develop a plan ‘‘for a physical environment adequate to promote the psychological well-being of primates.’’ In pursuing this charge, housing attributes such as social companionship, opportunities to express species-typical behavior, suitable space for expanded locomotor activity, and nonstressful relationships with laboratory personnel are dimensions that have dominated the discussion. Regulators were careful not to direct a specific set of prescriptions (i.e., engineering standards) for the attainment of these goals, but to leave the design of the …

State-Of-The-Art Of 3d Cultures (Organs-On-A-Chip) In Safety Testing And Pathophysiology, Natalie Alépée, Anthony Bahinski, Mardas Daneshian, Bart De Wever, Alan Goldberg, Jan Hansmann, Thomas Hartung, John Haycock, Helena T. Hogberg, Lisa Hoelting, Jens M. Kelm, Suzanne Kadereit, Emily Mcvey, Robert Landsiedel, Marcel Leist, Marc Lübberstedt, Fozia Noor, Christian Pellevoisin, Dirk Petersohn, Uwe Pfannenbecker, Kerstin Reisinger, Tzutzuy Ramirez, Barbara Rothen-Rutishauser, Monika Schäfer-Korting, Katrin Zeilinger, Marie-Gabriele Zurich

in Vitro Research Models Collection

Integrated approaches using different in vitro methods in combination with bioinformatics can (i) increase the success rate and speed of drug development; (ii) improve the accuracy of toxicological risk assessment; and (iii) increase our understanding of disease. Three-dimensional (3D) cell culture models are important building blocks of this strategy which has emerged during the last years. The majority of these models are organotypic, i.e., they aim to reproduce major functions of an organ or organ system. This implies in many cases that more than one cell type forms the 3D structure, and often matrix elements play an important role. This …

Clinical Trials And Late-Stage Drug Development In Alzheimer’S Disease: An Appraisal From 1984 To 2014, L. S. Schneider, F. Mangialasche, S. Andreasen, H. Feldman, E. Giacobini, R. Jones, V. Mantua, P. Mecocci, L. Pani, B. Winblad, M. Kivipelto

Human Clinical Trials Collection

The modern era of drug development for Alzheimer's disease began with the proposal of the cholinergic hypothesis of memory impairment and the 1984 research criteria for Alzheimer's disease. Since then, despite the evaluation of numerous potential treatments in clinical trials, only four cholinesterase inhibitors and memantine have shown sufficient safety and efficacy to allow marketing approval at an international level. Although this is probably because the other drugs tested were ineffective, inadequate clinical development methods have also been blamed for the failures. Here, we review the development of treatments for Alzheimer's disease during the past 30 years, considering the drugs, …

Conscientious Objection To Harmful Animal Use Within Veterinary And Other Biomedical Education, Andrew Knight

Science Education and Alternative Methods Collection

Laboratory classes in which animals are seriously harmed or killed, or which use cadavers or body parts from ethically debatable sources, are controversial within veterinary and other biomedical curricula. Along with the development of more humane teaching methods, this has increasingly led to objections to participation in harmful animal use. Such cases raise a host of issues of importance to universities, including those pertaining to curricular design and course accreditation, and compliance with applicable animal welfare and antidiscrimination legislation. Accordingly, after detailed investigation, some universities have implemented formal policies to guide faculty responses to such cases, and to ensure that …

The Effects Of Electrolyte Chemical Composition, Concentration And Ph On The Electrochemical Redox Reactions, Sea Choi, Xiao-Ying Yu

STAR Program Research Presentations

Electrolyte composition, concentration, pH, ionic strength, and temperature have long been known to play a role in the interface of the electrode-electrolyte. However, detailed studies are not sufficient. Cyclic voltammetry (CV) is a widely used electrochemical technique for obtaining qualitative information in electroanalysis. CV is often the first experiment performed in an electrode surface in an electrochemical study. It measures the number of electrons transferred and intermediates formed during oxidation-reduction (redox) reactions by observing its current, intensity and position of peak potential with applied voltage. This is accomplished by using a three-electrode system including working electrode (WE), counter electrode (CE) …

The Effects Of Lipoxin A4 (Lxa4) On Neutrophil Biology In Sepsis, Benedict Wu

Graduate School of Biomedical Sciences Theses and Dissertations

During sepsis, neutrophils are inappropriately activated and have prolonged lifespans, thus becoming dysfunctional. Excessive neutrophil activation can lead to tissue injury while neutrophil dysfunction can lead to decreased free radical production and reduced phagocytosis, preventing the host from clearing preexisting infections. Lipoxin A4 (LXA4) is a specialized pro-resolution mediator which reduces neutrophil migration and expression of proinflammatory mediators. Intact neutrophil functions are critical for the host to efficiently clear invading pathogens. The effects of LXA4 on neutrophil function in sepsis have not been established. Using the cecal ligation and puncture (CLP) model of sepsis, LXA4 administered 1 h after sepsis …

Consensus Report On The Future Of Animal-Free Systemic Toxicity Testing, Marcel Leist, Nina Hasiwa, Costanza Rovida, Mardas Daneshian, David Basketter, Ian Kimber, Harvey Clewell, Tilman Gocht, Alan Goldberg, Francois Busquet, Anna-Maria Rossi, Michael Schwarz, Martin Stephens, Rob Taalman, Thomas B. Knudsen, James Mckim, Georgina Harris, David Pamies, Thomas Hartung

Experimentation Collection

Since March 2013, animal use for cosmetics testing for the European market has been banned. This requires a renewed view on risk assessment in this field. However, in other fields as well, traditional animal experimentation does not always satisfy requirements in safety testing, as the need for human-relevant information is ever increasing. A general strategy for animal-free test approaches was outlined by the US National Research Council’s vision document for Toxicity Testing in the 21st Century in 2007. It is now possible to provide a more defined roadmap on how to implement this vision for the four principal areas of …

Lost In Translation: Animal Models And Clinical Trials In Cancer Treatment, Isabella W.Y. Mak, Nathan Evaniew, Michelle Ghert

Human Clinical Trials Collection

Due to practical and ethical concerns associated with human experimentation, animal models have been essential in cancer research. However, the average rate of successful translation from animal models to clinical cancer trials is less than 8%. Animal models are limited in their ability to mimic the extremely complex process of human carcinogenesis, physiology and progression. Therefore the safety and efficacy identified in animal studies is generally not translated to human trials. Animal models can serve as an important source of in vivo information, but alternative translational approaches have emerged that may eventually replace the link between in vitro studies and …

The Role Of Mammalian Cyclin C In Stress Response And Thyroid Disease Progression, Kun Wang

Graduate School of Biomedical Sciences Theses and Dissertations

The cellular response to stress involves changes in gene expression programs as well as the remodeling of subcellular organelles including the mitochondria. Important for this study, the mitochondria undergo extensive fragmentation when the cell is exposed to a variety of stressors. The cyclin C-Cdk8 kinase is a highly conserved transcription factor that associates with the RNA polymerase II holoenzyme. Using cyclin C knockout (CCNC^-/-) mouse embryonic fibroblast (MEF) cells, I revealed that cyclin C is required for the extensive mitochondrial fragmentation following treatment with pro-oxidants or the anti-cancer drug cisplatin. However, Cdk8 is not required for this process …

Effects Of River Current Inflow On Dissolved Oxygen And Temperature Of Refuge Zones For Cisco In Lake Bemidji, Bryant C. Swenson

Journal of Earth and Life Science

The objectives of this study were to (1) determine if the inflow current from the Mississippi River affects temperature and dissolved oxygen in Lake Bemidji, (2) determine how the amount of suitable cisco Coregonus artedi habitat changes over the summer in Lake Bemidji, and (3) predict how much cisco habitat would be available under a climate warming scenario. Summer fish kill of cisco occurs in most years on Lake Bemidji resulting from low dissolved oxygen in the hypolimnion and high water temperatures in the epilimnion. Dissolved oxygen and temperature profiles provided evidence to suggest the north basin is more suitable …

The Effect Of Barometric Pressure On Feeding Activity Of Yellow Perch, Daniel Vanderweyst

Journal of Earth and Life Science

This is the first study to our knowledge that has attempted to relate feeding activity of fish to barometric pressure. This study was conducted with the expectation that a difference in food ingestion would occur in a game fish species at different barometric pressures. The overall objective of this study is to determine if barometric pressure influences the feeding activity of a popular game fish. Yellow perch (Perca flavescens) were collected by seine and trap net from Lake Bemidji 12 September through 24 October 2013. The range in size and weight of yellow perch used for this study …

Use Of Cast Nets And Seine Hauls To Estimate Abundance Of Age-0 Yellow Perch, Michael Vaske

Journal of Earth and Life Science

Knowledge about fish population dynamics is essential for developing management plans and evaluating management success. In many lakes, yellow perch (Perca flavescens) are the main forage for many upper level predators and recreational fish species. To better manage recreational fisheries, an accurate estimate of prey abundance is necessary. The objectives of the study were to sample the littoral and limnetic zone to better estimate population of age-0 yellow perch, and obtain an estimate of the proportion of yellow perch being missed by traditional littoral seining methods. Littoral seines were conducted at three randomly selected locations in the south …

Changing Body Condition In Walleye With Reference To Ideal Sample Size Requirements, Kevin Longtin

Journal of Earth and Life Science

The objective of this study was to determine if walleye Sander vitreus percent dry weight, a measure of condition, differed among summer months of 2014 on Maple Lake, Minnesota. A second objective was to determine if there was a relationship between condition and body temperature, total length, or wet weight. Between three and six walleyes were collected per month by hook and line methods. All fish had internal body temperatures taken at the time of capture and were oven dried in the laboratory at 80 °C in order to measure percent dry weight. There was no relationship between condition and …

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 …

Defining The Physiochemical, Biological And Habitat Requirements For The Upper Extant Of Oncorhynchus Mykiss Distribution, Emily Powers

Journal of Earth and Life Science

The distribution of rainbow trout is strongly influenced by their habitat. As climatic conditions change, the distribution of rainbow trout populations will change along with them. The objective of this study was to identify the particular habitat parameters that rainbow trout select for in this lotic system and to specifically assess how this relates to the upper extant of their distribution. By assessing the distribution of the upper extant specifically, future research may be conducted to better assess climatic changes on a small and/or large scale basis. A 9,000 m section of the Clearwater River was used as the study …

The Effects Of Angling Pressure On Northern Pike Size Structure, Ryan Carrow

Journal of Earth and Life Science

A number of conditions within a lake system can affect northern pike (Esox lucius) size structure. Of these conditions, the amount of angling pressure may have the biggest effect on the size structure of northern pike in Minnesota lake systems. In this study, five private and five public lakes were chosen near Bemidji, Minnesota. Each lake was fished for twenty angling hours using live northern hog suckers (Hypentelium nigricans) or golden shiners (Notemigonus crysoleucas). Total length (mm) and weight (kg) were measured for each northern pike caught. The number of fish houses that were …

The Prevalence And Effect Of Wolbachia Infection On The Brown Widow Spider (Latrodectus Geometricus), Brittany Dane' Arrington

College of Graduate Studies: Theses & Dissertations

Wolbachia was recently identified in the Brown Widow Spider (Latrodectus geometricus). This symbiont has not previously been found in this genus, therefore the consequences on the host’s population dynamics are unknown. The frequency of endosymbiont infection can provide insight into the population dynamics of the host as this bacteria is known to alter host life history. In my 1^st chapter I determine the prevalence of Wolbachia pipentis infection in in the Brown Widow Spider (Latrodectus geometricus) from five locations in the Southeastern United States. Infection frequency differed significantly among sampling locations, ranging from 20% to …

The Impact Of Dams On Nitrogen Cycling In The Messalonskee Stream, Rebecca K. Forgrave

Honors Theses

The Messalonskee Stream in central Maine has five hydroelectric dams on 16.6km. Each dam drastically changes the flow regime of the stream, dividing it into segments with different patterns of sediment settling and organic matter retention. I investigated how these disruptions impact nitrogen cycling, specifically nitrification rates above and below each dam. I expected higher nitrification rates above the dams, where levels of organic matter are higher, and lower rates below the dam where scouring removes organic matter and fine sediment from the streambed. I measured sediment nitrification rates with a nitrapyrin-inhibition assay and potential drivers of nitrification including sediment …

A Brief Elevation Of Serum Amyloid A Is Sufficient To Increase Atherosclerosis, Joel C. Thompson

Theses and Dissertations--Pharmacology and Nutritional Sciences

Cardiovascular disease is now the leading cause of death worldwide. Serum amyloid A (SAA), a positive acute phase reactant, along with C-reactive protein is used clinically as a marker of cardiovascular disease risk. However, recent data has shed light on a possible causal role of SAA in the development of atherosclerosis, the most pervasive form of cardiovascular disease. Several inflammatory diseases such as diabetes and obesity are known to confer increased risk of developing cardiovascular disease. Individuals with these diseases all have modest but persistent elevation of SAA. To determine if SAA caused the development of atherosclerosis, apoe^-/-chow …

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 …

Report And Recommendations Of The Balance Of Crop Research Working Group Of The National Agricultural Research, Extension, Education And Economics (Nareee) Advisory Board, Mark Mclellan, Leo Holt, Twilya L'Ecuyer, Robert Taylor, Julia Sabin, Milo Shult, Anne Marie Thro, Paul Heisey

Biology Faculty Publications and Presentations

In December of 2012, the President’s Council of Advisors on Science & Technology (PCAST) issued a report to the President on Agricultural Preparedness and the Agriculture Research Enterprise. The PCAST report recognizes the long-term history of public investment in agricultural research. The report also recognized significant private investment into agricultural research. Significantly, the report is adamant that the agricultural research enterprise is not prepared to meet the challenges of the 21st century. The report cited two reasons:

1. too little competitive research and
2. an imbalance of research priorities between private and public funding sources.

This report addresses the latter issue.

Members …

Pcb Effects On Development Of Behavior In Rats, Robert Witte

Honors Projects

Abstract

PCBs were originally used as industrial chemicals in many devices and applications, including electrical capacitors and transformers, lubricants, and sealants in buildings. PCBs have been investigated and their use has been slowly phased out starting in the U.S. in the 1970s. A worldwide ban was put on the use and manufacturing of PCB in 2001, however they remain in the food chain because of their lipophilic properties and their long half-life. Major sources of PCB include wild-life, fish, and other seafood. Individuals exposed to PCB during development can experience negative effects on neurobiological, cognitive, and behavior functioning in both …

Targeted Knockout Of Beclin-1 Reveals An Essential Function In Ovary And Testis, Thomas R. Gawriluk

Theses and Dissertations--Biology

An estimated 12% of couples worldwide are infertile. The contributing factor is approximately equal between men and women with nearly 25% diagnosed as idiopathic. Despite the increasing numbers of couples seeking assistance from infertility clinics, few molecular mechanisms have been identified for treatment. Autophagy is an evolutionarily conserved cellular process for bulk degradation and recycling of cytosolic components through the lysosome to maintain homeostasis. Several studies have observed increased levels of autophagy during ovarian folliculogenesis and gonadal steroidogenesis; however, no genetic studies to determine the significance of autophagy exist.

To investigate the function of autophagy in the ovary and testis, …