Biology Commons^™

Conflicting Evolutionary Histories Of The Mitochondrial And Nuclear Genomes In New World Myotis Bats, Thomas Lee Jr.

Biology

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred fromnuclear markers lackedresolution. Our current understanding of relationships withinMyotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this,we sequenced the full mitochondrial genomes of 37 representativeMyotis, primarily fromtheNewWorld, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic …

Differential Uptake Of Gold Nanoparticles By 2 Species Of Tadpole, The Wood Frog (Lithobates Sylvaticus) And The Bullfrog (Lithobates Catesbeianus), Lucas B. Thompson, Gerardo L.F. Carfagno, Kurt Andresen, Andrea J. Sitton, Taylor B. Bury, Laura L. Lee, Kevin T. Lerner, Peter P. Fong

Biology Faculty Publications

Engineered nanoparticles are aquatic contaminants of emerging concern that exert ecotoxicological effects on a wide variety of organisms. We exposed cetyltrimethylammonium bromide–capped spherical gold nanoparticles to wood frog and bullfrog tadpoles with conspecifics and in combination with the other species continuously for 21 d, then measured uptake and localization of gold. Wood frog tadpoles alone and in combination with bullfrog tadpoles took up significantly more gold than bullfrogs. Bullfrog tadpoles in combination with wood frogs took up significantly more gold than controls. The rank order of weight-normalized gold uptake was wood frogs in combination > wood frogs alone > bullfrogs in combination …

Breaking In And Busting Out: Cell-Penetrating Peptides And The Endosomal Escape Problem, Julia C. Lecher, Scott J. Nowak, Jonathan Mcmurry

Faculty Articles

Cell-penetrating peptides (CPPs) have long held great promise for the manipulation of living cells for therapeutic and research purposes. They allow a wide array of biomolecules from large, oligomeric proteins to nucleic acids and small molecules to rapidly and efficiently traverse cytoplasmic membranes. With few exceptions, if a molecule can be associated with a CPP, it can be delivered into a cell. However, a growing realization in the field is that CPP-cargo fusions largely remain trapped in endosomes and are eventually targeted for degradation or recycling rather than released into the cytoplasm or trafficked to a desired subcellular destination. This …

Itraq-Based Proteomics Analysis And Network Integration For Kernel Tissue Development In Maize, Long Zhang, Yongbin Dong, Qilei Wang, Chunguang Du, Wenwei Xiong, Xinyu Li, Sailan Zhu, Yuling Li

Department of Biology Faculty Scholarship and Creative Works

Grain weight is one of the most important yield components and a developmentally complex structure comprised of two major compartments (endosperm and pericarp) in maize (Zea mays L.), however, very little is known concerning the coordinated accumulation of the numerous proteins involved. Herein, we used isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic method to analyze the characteristics of dynamic proteomics for endosperm and pericarp during grain development. Totally, 9539 proteins were identified for both components at four development stages, among which 1401 proteins were non-redundant, 232 proteins were specific in pericarp and 153 proteins were specific in …

Allergen Homologs In The Euroglyphus Maynei Draft Genome, S. Dean Rider, Majorie S. Morgan, Larry G. Arlian

Biological Sciences Faculty Publications

Euroglyphus maynei is a house dust mite commonly found in homes worldwide and is the source of allergens that sensitize and induce allergic reactions in humans. It is the source of species-specific allergens as well as allergens that are cross-reactive with the allergens from house dust mites Dermatophagoides farinae and D. pteronyssinus, and the ectoparasitic scabies mite Sarcoptes scabiei. The genomics, proteomics and molecular biology of E. maynei and its allergens have not been as extensively investigated as those of D. farinae, D. pteronyssinus, and S. scabiei where natural and recombinant allergens from these species have been characterized. Until now, …

Geometric Morphometric Analysis Of The Pedal Claw Of The Early Cretaceous Bird Confuciusornis Sanctus (Confuciusornithidae) And Its Functional And Behavioral Implications, Annie P. Mcintosh

College of Science and Health Theses and Dissertations

onfuciusornis sanctus (Hou et al., 1995) is an Early Cretaceous bird from the Liaoning Province of northeastern China. Much work has been published on this species, but some details of its habitat and behavior remain unclear. In this study, a geometric morphometric analysis of the ungual of the second pedal digit of Confuciusornis sanctus was performed to determine how its morphology compares to that of extant birds and which morphological variables best distinguish between taxonomic and behavioral groups. A total of 128 specimens was examined, comprising 104 extant bird species across 15 orders and Confuciusornis sanctus. Three fixed landmarks and …

Egg Morphology, Dispersal, And Transmission In Acanthocephalan Parasites: Integrating Phylogenetic And Ecological Approaches, Alana C. Pfenning

College of Science and Health Theses and Dissertations

Acanthocephalans are endoparasites that infect arthropods as intermediate hosts and vertebrates as definitive hosts and are found in diverse habitats (freshwater, marine, terrestrial) throughout the world. Free-living eggs are expelled from the definitive host into the environment, which are then consumed by an intermediate host. Once ingested by the intermediate host the parasite undergoes a series of developmental stages, the final stage is infectious to the definitive host. Transmission to a definitive host occurs when the predator consumes an intermediate host containing an infectious parasite. The parasites reach sexual maturity within the definitive host. Most research to date has focused …

Food Addiction And The Effective Treatment Of Adult Food Addicts: An Integrative Review Of Literature, Sara Bourque

Grace Peterson Nursing Research Colloquium

Abstract

Background: In a survey conducted between the years of 2011 and 2014 it was suggested that 36% of adults in the U.S. were obese with over 40.2% being middle aged adults. Obesity is associated with a number of comorbid conditions including diabetes, heart attacks, and strokes. Due to this it is one of the major factors driving up our annual medical care costs. It is also one of the leading causes of death not only in the U.S. but worldwide. With one third of the adult population in the U.S. being obese food addiction may very well be a …

The Heat Shock Response And Humoral Immune Response Are Mutually Antagonistic In Honey Bees, Mia Mckinstry, Charlie Chung, Henry Truong, Brittany A. Johnston, Jonathan W. Snow

Publications and Research

The honey bee is of paramount importance to humans in both agricultural and ecological settings. Honey bee colonies have suffered from increased attrition in recent years, stemming from complex interacting stresses. Defining common cellular stress responses elicited by these stressors represents a key step in understanding potential synergies. The proteostasis network is a highly conserved network of cellular stress responses involved in maintaining the homeostasis of protein production and function. Here, we have characterized the Heat Shock Response (HSR), one branch of this network, and found that its core components are conserved. In addition, exposing bees to elevated temperatures normally …

Choline Supplementation Normalizes Fetal Adiposity And Reduces Lipogenic Gene Expression In A Mouse Model Of Maternal Obesity, Chauntelle Jack-Roberts, Yaelle Joselit, Khatia Nanobashvili, Rachel Bretter, Olga V. Malysheva, Marie A. Caudill, Anjana Saxena, Kathleen Axen, Ahmed Gomaa, Xinyin Jiang

Publications and Research

Maternal obesity increases fetal adiposity which may adversely affect metabolic health of the offspring. Choline regulates lipid metabolism and thus may influence adiposity. This study investigates the effect of maternal choline supplementation on fetal adiposity in a mouse model of maternal obesity. C57BL/6J mice were fed either a high-fat (HF) diet or a control (NF) diet and received either 25 mM choline supplemented (CS) or control untreated (CO) drinking water for 6 weeks before timed-mating and throughout gestation. At embryonic day 17.5, HF feeding led to higher (p < 0.05) percent total body fat in fetuses from the HFCO group, while the choline supplemented HFCS group did not show significant difference versus the NFCO group. Similarly, HF feeding led to higher (p < 0.05) hepatic triglyceride accumulation in the HFCO but not the HFCS fetuses. mRNA levels of lipogenic genes such as Acc1, Fads1, and Elovl5, as well as the transcription factor Srebp1c that favors lipogenesis were downregulated (p < 0.05) by maternal choline supplementation in the HFCS group, which may serve as a mechanism to reduce fat accumulation in the fetal liver during maternal HF feeding. In summary, maternal choline supplementation improves indices of fetal adiposity in obese dams at late gestation.

Effects Of Cultivar And Maternal Environment On Seed Quality In Vicia Sativa, Rong Li, Lijun Chen, Yanpei Wu, Rui Zhang, Carol C. Baskin, Jerry M. Baskin, Xiaowen Hu

Biology Faculty Publications

Production of high quality seeds is of fundamental importance for successful crop production. However, knowledge of the effects of increased temperature resulting from global warming on seed quality of alpine species is limited. We investigated the effect of maternal environment on seed quality of three cultivars of the leguminous forage species Vicia sativa, giving particular attention to temperature. Plants of each cultivar were grown at 1700 and 3000 m a.s.l., and mass, germination, electrical conductivity (EC) of leakage and longevity were determined for mature seeds. Seeds of all three cultivars produced at the low elevation had a significantly lower …

Expanding Metabolic Diversity Of Two Archaeal Phyla: Nanoarchaeota And Korarchaeota, John Forad Kelley

Dissertations and Theses

Culture independent studies have revealed a greater diversity of Archaea than the two kingdoms initially defined by Carl Woese. Culturing species from the newly discovered archaeal lineages, as with the majority of microbes, has been difficult. To overcome the culturing dilemma, metagenomics is being used to reconstruct environmental genomes. Two metagenomic studies are presented in this thesis, with the aim of recovering newly proposed archaeal genomes from the Nanoarchaeota and Korarchaeota.

In the first study, a sediment sample, NZ13, was collected from a terrestrial New Zealand hot spring. Along with the sediment sample, two complex enrichments were sequenced on an …

Biophysical And Computational Studies Of The Vcci:Vmip-Ii Complex, Anna Nguyen, Nai-Wei Kuo, Laura Showalter, Ricardo Ramos, Cynthia Dupureur, Michael Colvin, Patricia Liwang

Chemistry & Biochemistry Faculty Works

Certain viruses have the ability to subvert the mammalian immune response, including interference in the chemokine system. Poxviruses produce the chemokine binding protein vCCI (viral CC chemokine inhibitor; also called 35K), which tightly binds to CC chemokines. To facilitate the study of vCCI, we first provide a protocol to produce folded vCCI from Escherichia coli (E. coli.) It is shown here that vCCI binds with unusually high affinity to viral Macrophage Inflammatory Protein-II (vMIP-II), a chemokine analog produced by the virus, human herpesvirus 8 (HHV-8). Fluorescence anisotropy was used to investigate the vCCI:vMIP-II complex and shows that vCCI binds to …

Autoantibodies As Diagnostic Biomarkers For The Detection And Subtyping Of Multiple Sclerosis, Cassandra Demarshall, Eric Goldwaser, Abhirup Sarkar, George Godsey, Nimish Acharya, Umashanger Thayasivam, Benjamin Belinka, Robert Nagele

Rowan-Virtua School of Osteopathic Medicine Departmental Research

The goal of this preliminary proof-of-concept study was to use human protein microarrays to identify blood-based autoantibody biomarkers capable of diagnosing multiple sclerosis (MS). Using sera from 112 subjects, including 51 MS subjects, autoantibody biomarkers effectively differentiated MS subjects from age- and gender-matched normal and breast cancer controls with 95.0% and 100% overall accuracy, but not from subjects with Parkinson's disease. Autoantibody biomarkers were also useful in distinguishing subjects with the relapsing-remitting form of MS from those with the secondary progressive subtype. These results demonstrate that autoantibodies can be used as noninvasive blood-based biomarkers for the detection and subtyping of …

Seasonal Ecology Of Mottled Sculpin And Brown Trout In A Coldwater Michigan Stream, Susanna K. Lagory

Masters Theses

In temperate regions, environmental conditions vary distinctly between seasons. This variation can strongly impact in-stream environmental conditions. Winter is often thought to be harsher than other seasons for stream fishes, given the adverse environmental conditions that arise from low temperatures during winter in temperate regions. Low temperatures, episodic elevated discharge, and ice formation associated with winter are hypothesized to reduce movement, body condition, and survival of stream fishes. However, few studies test this hypothesis through formal comparisons, and most studies of seasonal stream fish ecology focus on salmonids. To address this knowledge gap, I estimated and compared body condition, net …

Polychlorinated Biphenyl Concentrations In Fish From Lake Michigan Tributaries And A Preliminary Risk Assessment Concerning Their Consumption By Sport And Tribal Fishermen, Amanda K. Potter

Masters Theses

Human and environmental health continues to be threatened by persistent organic pollutants in the Great Lakes ecosystem. Polycholorinated biphenyls (PCBs) are considered one of the most toxic contaminants in the Great Lakes due to their recalcitrance, bioaccumulation, lipid solubility, and adverse health effects.

The three main questions examined in this research were: 1) Do PCB concentrations vary between largemouth bass (Micropterus salmoides), northern pike (Esox Lucius), smallmouth bass (Micropterus dolomieu), and walleye (Sander vitreus) in west Michigan tributaries of Lake Michigan; 2) Do PCB concentrations vary on a watershed level among Manistee …

Yellow Perch Genetic Stock Structure In Eastern Lake Michigan: What Is The Importance Of Drowned River Mouth Lakes?, Gregory M. Chorak

Masters Theses

Habitat heterogeneity has the possibility of structuring populations. Even in connected landscapes, there can be cryptic structuring of populations that coincides with landscape features that limit gene flow or select for different phenotypes within a species. Yellow perch (Perca flavescens) is an economically and ecologically prominent fish in the Laurentian Great Lakes. In the Lake Michigan basin, yellow perch reside in nearshore Lake Michigan, including drowned river mouths (DRMs, lake-like habitats that link tributaries to Lake Michigan). The goal of this study was to understand whether yellow perch populations are structured in eastern Lake Michigan by the connected …

Understanding The Relationship Between Hosts And Their Microbiome, Boahemaa Adu-Oppong

Arts & Sciences Graduate Student Theses and Dissertations

Microbes are bountiful and associated with every animal and plant kingdom. Furthermore, microbes can alter host phenotype, development, health and functioning. However, this is not a one-way interaction, hosts can structure microbial communities by changing the environment to be suitable for certain microbial species. Several studies have characterized microbial communities associated with hosts to answer two2 main questions in ecology: who’s there, and what are they doing? However, two questions from the field of community ecology are often ignored (1) what forces are structuring the microbial communities (how was the community formed) and (2) how stable are these communities. Vellend …

Mechanisms And Regulation Of Resection In Dna Damage Response, Sharad C. Paudyal

Arts & Sciences Graduate Student Theses and Dissertations

Deoxyribonucleic acid (DNA) encodes genetic information essential for cell survival and function. However, it is constantly under assault from endogenous and exogenous damaging agents that not only threaten our own survival but also affect the faithful transmission of genetic information to our offspring. Double-strand breaks (DSBs) are one of the most hazardous forms of DNA damage, which if unrepaired or improperly repaired could lead to plethora of systemic human diseases including cancer. To deal with this problem, cells have evolved with a mechanism called DNA damage response (DDR) to detect, signal, and repair the breaks by inducing multiple cellular events. …

Designing Epigenome Editing Tools To Understand The Functional Role Of Dna Methylation Changes In Cancer, James Mcdonald

Arts & Sciences Graduate Student Theses and Dissertations

DNA methylation is known to silence gene expression in the context of imprinting, X-chromosome inactivation, and retrotransposon silencing. However, the role of DNA methylation in silencing gene expression outside of these contexts is not fully understood. This is especially true in diseases such as cancer, where normal DNA methylation patterns are significantly altered. In breast cancer as well as nearly all cancer types, most of the genome loses DNA methylation while small regions of the genome gain methylation. DNA methylation generally correlates with decreased gene expression when present at a gene promoter. Therefore, these regions of hypo- and hyper-methylation may …

Characterization And Function Of Islet Antigen Presenting Cells During Nod Diabetes, Stephen Thomas Ferris

Arts & Sciences Graduate Student Theses and Dissertations

Here we characterized the initial antigen presenting cells (APCs) within the islet of Langerhans to ascertain their identity and functional role as it pertains to autoimmune diabetes. The activation of the adaptive immune system is induced by the innate immune system, and more specifically APCs. Therefore, it is crucial to identify the APCs that are initiating T1D in order to elucidate the break in tolerance and intervene in order to inhibit progression. We have found that there is a resident macrophage that is present in all strains of mice. This islet macrophage has a distinct transcriptional profile that is unique …

Antiviral Nucleoside Inhibitors Of Leishmania Rna Virus 1: Discovery And Mechanism, John Isaac Robinson

Arts & Sciences Graduate Student Theses and Dissertations

Some Leishmania parasites in the Viannia sub-genus are persistently infected with Leishmania RNA virus 1 (LRV1), a single-segmented double-stranded RNA virus belonging to the family Totiviridae. Infected parasites cause greater pathology and reach higher populations in mouse models of Leishmania infection. In human disease, LRV1+ parasites are correlated with increased frequency of treatment failure and relapse. Efficient methods to detect LRV1 and eliminate it from parasites are required to better understand the role of LRV1 in Leishmania infection. We optimized multiple techniques to measure LRV1 levels in parasites, most notably using flow cytometry to measure the amount of viral capsid …

Exploring Host-Virus Interactions In Caenorhabditis Nematodes, Kevin Chen

Arts & Sciences Graduate Student Theses and Dissertations

Caenorhabditis elegans is a powerful model organism that has elucidated many biological questions in the fields of genetics, development, and neurobiology. In addition, C. elegans has been used in the past decade to investigate host-pathogen interactions with bacteria and fungi. The recent identification of nematode viruses that naturally infect C. elegans and Caenorhabditis briggsae provides a unique opportunity to define host-virus interactions in these model hosts.This dissertation first explored the transcriptional response of C. elegans and C. briggsae to virus infection by RNA-seq. I identified a total of 320 differentially expressed genes (DEGs) in C. elegans following Orsay virus infection. …

Specificity Determination By Paralogous Winged Helix-Turn-Helix Transcription Factors, Adam Joyce

Arts & Sciences Graduate Student Theses and Dissertations

Transcription factors (TFs) localize to regulatory regions throughout the genome, where they exert physical or enzymatic control over the transcriptional machinery and regulate expression of target genes. Despite the substantial diversity of TFs found across all kingdoms of life, most belong to a relatively small number of structural families characterized by homologous DNA-binding domains (DBDs). In homologous DBDs, highly-conserved DNA-contacting residues define a characteristic ‘recognition potential’, or the limited sequence space containing high-affinity binding sites. Specificity-determining residues (SDRs) alter DNA binding preferences to further delineate this sequence space between homologous TFs, enabling functional divergence through the recognition of distinct genomic …

Brain Enriched Micrornas Open The Neurogenic Potential Of Adult Human Fibroblasts, Daniel Gene Abernathy

Arts & Sciences Graduate Student Theses and Dissertations

The seemingly limitless capacities of mammals to sense, respond, and manipulate their environments stems from their structurally and functionally diverse nervous systems. Establishing these complex behaviors requires the integration of many biological phenomena including, morphogenetic gradients, cell-cell signaling, transcriptional networks, cell migration and epigenetic gene regulation. As mammalian development progresses, these pathways coordinate the production of highly specialized neuronal and glial cells, that connect and communicate with another in an even more complex manner. While evolution has shaped a multitude of pathways to produce numerous favorable traits, it has also created an intricate system vulnerable to disease. The loss of …

Identification And Characterization Of An Interferon Stimulated Gene That Restricts Alphavirus Infection And Pathogenesis, Subhajit Poddar

Arts & Sciences Graduate Student Theses and Dissertations

Viral infection of host cells induces the Type I interferon (IFN) response, which ischaracterized by the production of hundreds of IFN-stimulated genes (ISGs). Altogether, theseISGs function to induce an antiviral state, hindering or blocking various steps of the virallifecycle. Many individual ISGs have potent and broad antiviral functions. However eliminationof a single ISG does not completely abrogate protection, suggesting that other ISGs, althoughmoderate or moderate when considered alone, must work cooperatively to provide optimalantiviral activity.In order to identify and characterize novel ISGs, an attenuated strain of the alphaviruschikungunya (CHIKV-181/25) was tested against an shRNA library of 243 curated murine genesupregulated …

Nuclear Export Factor 3 Regulates The Localization Of Small Nucleolar Rnas, Melissa Wanling Li

Arts & Sciences Graduate Student Theses and Dissertations

Metabolic diseases, such as obesity and diabetes, are associated with excess levels of lipids, which can lead to organelle dysfunction, cell death and eventually organ dysfunction. This process, termed lipotoxicity, is still not completely understood. In a genetic screen used to identify genes critical for lipotoxicity, the Schaffer lab has identified small nucleolar RNAs (snoRNAs) within the ribosomal protein L13a (Rpl13a) locus that mediate the cellular response to lipotoxic and general metabolic stress. These snoRNAs are non-canonical in that they accumulate in the cytosol after metabolic stresses like lipotoxicity and oxidative stress, suggesting that cells have specific mechanisms for regulating …

The Effect Of Dietary Fat On Obesity, Gene Expression, And Dna Methylation In Two Generations Of Mice, Madeline Rose Keleher

Arts & Sciences Graduate Student Theses and Dissertations

As obesity rates continue rising nationally and globally, it is crucial to understand how a high-fat diet disrupts the regulation of the genome and leads to adverse health effects. Uncovering the underlying gene expression and DNA methylation changes induced by an individual’s high-fat diet and a maternal high-fat diet can pinpoint new targets for epigenetic therapies and reveal the physiological and behavioral changes in obesity. The goal of this dissertation is to gain deeper insight into the DNA methylation and gene expression changes that occur in response to a high-fat diet.I studied the response to dietary fat within two generations …

Dna Replication Challenges: Telomeres And R Loops, Shankar Parajuli

Arts & Sciences Graduate Student Theses and Dissertations

Faithful DNA replication and repair are essential for maintaining genome stability and preventing various diseases including cancer. Both processes are executed by numerous redundant mechanisms to ensure that these processes are uninterrupted even when a primary mechanism fails. Despite this, they are not immune to challenges and failures leading to DNA damage and genome instability. These problems are more evident at the difficult-to-replicate regions of the genome such as the telomeres that cap and protect linear chromosome ends. Additionally, topological structures such as RNA:DNA hybrids, commonly referred to as R loops, can also present severe challenges to the DNA replication …

Investigation Of The Contribution Of Type 1 Pili In Enterotoxigenic Escherichia Coli (Etec) Pathogen-Host Interactions, Alaullah Sheikh

Arts & Sciences Graduate Student Theses and Dissertations

Enterotoxigenic Escherichia coli (ETEC) are one of the leading causes of death due to diarrhea in children living in developing countries. ETEC are also the leading cause of diarrhea in travelers to developing countries lacking sanitation and safe drinking water. Unfortunately, there is no broadly protective vaccine available against these important pathogens. In order to cause infection, ETEC colonize the intestinal epithelium and secrete toxins, including heat-labile toxin (LT) and/or heat-stable toxin (ST). Efficient delivery of these toxins to the cognate receptors on target intestinal cells requires direct ETEC-host interactions. Earlier studies demonstrated that ETEC facilitate interactions with host by …