Biology Commons^™

Expression And Function Of Snornas In Acute Myeloid Leukemia, Wayne Alsworth Warner

Arts & Sciences Graduate Student Theses and Dissertations

Small nucleolar RNAs (snoRNAs) are non-coding RNAs that contribute to ribosome biogenesis and RNA splicing by modifying ribosomal RNA and spliceosome RNAs, respectively. These modifications are critical for a variety of cellular processes, including ribosomal biogenesis and splicing of RNAs. Recent studies have suggested an expanded role for snoRNAs beyond ribosomal biogenesis and splicing, including, regulation of chromatin structure, metabolism, and neoplastic transformation. The contribution of snoRNAs to the regulation of normal and malignant hematopoiesis is largely unknown. The lack of a method to accurately and comprehensively assess snoRNA expression has limited research in this area. In particular, array-based methods …

Understanding Excitation Energy Quenching In Isia, Hui-Yuan Steven Chen

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cyanobacteria are photoautotrophic organisms that contribute a significant amount of global primary productivity. They are found in freshwater, marine and even some extremely severe environments. Among those environments, iron deficiency is one of the most common stress conditions in cyanobacterial habitats. To survive, cyanobacteria have evolved and developed several strategies to alleviate the damage caused by iron deficiency.

Iron stress-inducible protein (IsiA) is a chlorophyll-binding membrane protein found in cyanobacteria grown in iron-deficient conditions. During the past decades, considerable effort has been put on understanding how IsiA functions to help cyanobacteria survive iron deficiency. It has been reported that IsiA …

Individual Differences In Human Brain Functional Network Organization, Benjamin A. Seitzman

Arts & Sciences Graduate Student Theses and Dissertations

The human brain is organized at many spatial scales, including the level of areas and systems. Resting-state functional magnetic resonance imaging is a non-invasive technique that allows for the study of areal- and systems-level brain organization in vivo. Over two decades of research has sought to identify and characterize the functional communities that comprise the brain’s network architecture. Consequently, a convergent description of group-average functional network organization in healthy adults has emerged. Recent advances have allowed for the study of such organization in single individuals. Investigation of functional network organization in highly sampled individuals has revealed brain regions that deviate …

Determining The Genetic Contributions Of The Williams Syndrome Critical Region To Behavior Using Mouse Models And Human Genetics, Nathan David Kopp

Arts & Sciences Graduate Student Theses and Dissertations

Williams syndrome is a neurodevelopmental model caused by the deletion of 26-28 genes on chr7q11.23. The loss of these genes affects multiple organ systems resulting in severe cardiovascular disease, craniofacial dysmorphology, intellectual impairment, a specific Williams syndrome cognitive profile made up of deficits in visual-spatial processing with preserved language skills, and a characteristic hypersocial personality. The reciprocal duplication occurs at a lower frequency and manifests with diametric phenotypes to the deletion. This suggests that this locus harbors dosage sensitive genes that play a role in neurodevelopment. Large efforts have been taken to identify which genes are responsible for causing the …

Aging Of The Reproductive System And Of Germline Stem Cells In Caenorhabditis, Zuzana Kocsisova

Arts & Sciences Graduate Student Theses and Dissertations

C. elegans hermaphrodites display dramatic age-related decline of reproduction early in life while somatic functions are still robust. To understand why the germline fails so early, we analyzed the assembly line of oocyte production that generates fertilized eggs in mated hermaphrodites with sufficient sperm. Aging germlines displayed both sporadic and population-wide changes. A small fraction of aging animals displayed endomitotic oocytes in the germline and other defects. By contrast, all animals displayed age-related decreases in germline size and function. As early as day 3 of adulthood, animals displayed fewer stem cells and a slower cell cycle, which combine to substantially …

Determining The Genetic Contributions Of The Williams Syndrome Critical Region To Behavior Using Mouse Models And Human Genetics, Nathan David Kopp

Arts & Sciences Graduate Student Theses and Dissertations

Williams syndrome is a neurodevelopmental model caused by the deletion of 26-28 genes on chr7q11.23. The loss of these genes affects multiple organ systems resulting in severe cardiovascular disease, craniofacial dysmorphology, intellectual impairment, a specific Williams syndrome cognitive profile made up of deficits in visual-spatial processing with preserved language skills, and a characteristic hypersocial personality. The reciprocal duplication occurs at a lower frequency and manifests with diametric phenotypes to the deletion. This suggests that this locus harbors dosage sensitive genes that play a role in neurodevelopment. Large efforts have been taken to identify which genes are responsible for causing the …

High-Density Diffuse Optical Tomography During Passive Movie Viewing: A Platform For Naturalistic Functional Brain Mapping, Andrew Kelsey Fishell

Arts & Sciences Graduate Student Theses and Dissertations

Human neuroimaging techniques enable researchers and clinicians to non-invasively study brain function across the lifespan in both healthy and clinical populations. However, functional brain imaging methods such as functional magnetic resonance imaging (fMRI) are expensive, resource-intensive, and require dedicated facilities, making these powerful imaging tools generally unavailable for assessing brain function in settings demanding open, unconstrained, and portable neuroimaging assessments. Tools such as functional near-infrared spectroscopy (fNIRS) afford greater portability and wearability, but at the expense of cortical field-of-view and spatial resolution. High-Density Diffuse Optical Tomography (HD-DOT) is an optical neuroimaging modality directly addresses the image quality limitations associated with …

Mechanism Of Activation Of Uvrd Helicase By A Processivity Factor Mutl, Yerdos Ordabayev

Arts & Sciences Graduate Student Theses and Dissertations

E. coli UvrD is a superfamily 1A helicase/translocase involved in DNA repair, recombination, and replication. I investigated the role of E. coli MutL, a regulatory protein involved in methyl-directed mismatch DNA repair, in the regulation of UvrD-catalyzed DNA unwinding. Using single molecule fluorescence resonance energy transfer (FRET) and single round stopped-flow DNA unwinding experiments I demonstrated that MutL can activate latent UvrD monomer helicase activity and also stimulate UvrD dimer helicase activity. Furthermore, using analytical ultracentrifugation experiments I determined that a single MutL dimer is sufficient to activate UvrD monomer helicase. DNA unwinding experiments with a series of DNA substrates …

Visual And Chemosensory Pathways Associated With Male Courtship Decisions In Drosophila Melanogaster, Ross Mckinney

Arts & Sciences Graduate Student Theses and Dissertations

Successful mating in diverse animal species often depends on ritualistic sequences of spatially and temporally coordinated behavioral elements. Yet, the sensory cues and neural circuits that mediate optimal mating display patterns are largely unknown. The courtship ritual in Drosophila melanogaster consists of a well-studied sequence of behavioral elements — including orienting, chasing, tapping, singing, and licking — that are known to depend on several sensory modalities, including both vision and chemosensation. However, the specific sensory inputs utilized by males to direct the spatial and temporal transitions between different elements of the courtship ritual are not well understood. In this thesis, …

Brain Blood Flow And Metabolism: Variable Relationships In Altered Metabolic States, Tyler M. Blazey

Arts & Sciences Graduate Student Theses and Dissertations

Brain metabolism is usually thought of in terms of energy production. Decades of research has shown that the brain derives the majority of its energy from the oxidative phosphorylation of glucose transported from the blood into the brain. Because of this, cerebral blood flow (CBF), the cerebral metabolic rate of glucose consumption (CMRglc), and the cerebral metabolic rate of oxygen consumption (CMRO2) generally are tightly coupled. Indeed, the coupling between CBF, CMRglc, and CMRO2 is robust enough such that many investigators believe them to be equivalent measures of brain activity.Nevertheless, research over the last few decades has shown that cerebral …

Understanding The Transcriptional Mechanisms Underlying Dendritic Cell Development, Prachi Bagadia

Arts & Sciences Graduate Student Theses and Dissertations

Dendritic cells (DCs) comprise an important immune lineage that plays a critical role in initiating and sustaining the proper immune response. They can be divided into two distinct branches, classical/conventional DCs (cDCs) or plasmacytoid DCs (pDCs). cDCs can further be classified as cDC1 or cDC2. Each DC subset exerts unique functions in vivo and are necessary for a complete immune response.The precise transcriptional programs underlying DC specification and commitment remain unclear. cDC1, cDC2, and pDC all arise from the common DC progenitor (CDP) in the bone marrow. How the CDP gives rise to all three DC subsets in an important …

The Role Of Mitofusins In The Osteoclast Lineage, Anna Ballard

Arts & Sciences Graduate Student Theses and Dissertations

Mitochondria exist in a highly dynamic network in many cell types, and mutations in mitochondrial transmembrane GTPase mitofusin2 (MFN2), a key factor that mediates mitochondrial tethering, cause defects in the nervous system. Intriguingly, the skeleton has been overlooked in patients with such mutations. Because expression of MFN2 and its homolog, mitofusin1 (MFN1) increase with maturation of osteoclasts (OCs), which are rich in mitochondria, we sought to determine the role of mitofusins in the OC lineage. Double knockout of Mfn1 and Mfn2 in OC precursors by Lysozyme-M cre reveals that mitofusin activity is required for OC function and maintenance of bone …

Multi-Omic Understanding Of The Evolution Of Xenobiotic Tolerance In Bacterial Isolates And Communities, Tayte Paul Campbell

Arts & Sciences Graduate Student Theses and Dissertations

Xenobiotic compounds are any chemicals that are released into an environment by human action and that occur at concentrations higher than found naturally. Xenobiotics, including aromatic compounds and antibiotics, are recalcitrant to degradation because they are often toxic or mutagenic. Despite this toxicity, bacteria account for a large portion of xenobiotic degradation in the environment. Bacteria are able to adapt to these foreign chemicals, gaining increased levels of tolerance and increased rates of xenobiotic degradation. On the strain level, increased tolerance can be caused by mutations in individual cells or through the acquisition of genes from other cells. At the …

High-Density Diffuse Optical Tomography During Passive Movie Viewing: A Platform For Naturalistic Functional Brain Mapping, Andrew Kelsey Fishell

Arts & Sciences Graduate Student Theses and Dissertations

Human neuroimaging techniques enable researchers and clinicians to non-invasively study brain function across the lifespan in both healthy and clinical populations. However, functional brain imaging methods such as functional magnetic resonance imaging (fMRI) are expensive, resource-intensive, and require dedicated facilities, making these powerful imaging tools generally unavailable for assessing brain function in settings demanding open, unconstrained, and portable neuroimaging assessments. Tools such as functional near-infrared spectroscopy (fNIRS) afford greater portability and wearability, but at the expense of cortical field-of-view and spatial resolution. High-Density Diffuse Optical Tomography (HD-DOT) is an optical neuroimaging modality directly addresses the image quality limitations associated with …

Regulation Of The Yeast Cell Cycle Checkpoint Kinase Tel1 At Double-Strand Dna Breaks And At Telomeres, Sarem Hailemariam

Arts & Sciences Graduate Student Theses and Dissertations

The work discussed in this dissertation focuses on two distinct areas that are critical for genome maintenance. Both areas are focused on the regulation of the Saccharomyces cerevisiae checkpoint kinase Tel1 by the MRX complex. Tel1 kinase initiates cell cycle checkpoint in response to double-strand DNA breaks. Tel1 also plays a major role in telomere maintenance. Tel1’s function both in checkpoint signaling and telomere regulation is dependent on the Mre11-Rad50-Xrs2 complex. In Chapter II, I describe a robust biochemical approach aimed at reconstituting the initial stages of double-strand DNA break response using purified proteins in order to address how the …

Genomic Signatures Of Conflict And Cooperation In Plants And Social Amoebae, Katherine Sylvia Geist

Arts & Sciences Graduate Student Theses and Dissertations

Arms races involve bouts of reciprocal co-adaptation to a social environment. We have a strong sense for how arms races drive the evolution of genes in purely antagonistic contexts, such as host-pathogen or predator-prey. In these systems, conflict that produces arms races between two parties results in positive selection – the fixation of adaptive alleles between species – for both parties. However, we do not have an equal sense for how arms races during cooperative enterprises shape genic evolution. If we assume that arms races affect genic evolution similarly regardless of context – antagonistic or cooperative – then we would …

Understanding The Physiology Of Extracellular Electron Uptake In Purple Nonsulfur Bacteria, Michael Singh Guzman

Arts & Sciences Graduate Student Theses and Dissertations

Microbially catalyzed oxidation-reduction reactions drive nutrient cycling and energy flux on Earth. Photoautotrophs, which include the cyanobacteria (oxygenic) and purple and green sulfur bacteria (anoxygenic), transform light energy into chemical energy and are responsible for substantial global primary productivity. Anoxygenic phototrophs, in particular, play a crucial role in biogeochemical cycling in anoxic illuminated environments because of their ability to oxidize an array of inorganic compounds for CO2 fixation. Electron donors include molecular hydrogen, nitrite, and reduced sulfur compounds. Recent evidence has also suggested that solid-phase conductive substances (SPCSs), including rust (mixed-valent iron minerals) and their proxies (poised electrodes), can serve …

Visual And Chemosensory Pathways Associated With Male Courtship Decisions In Drosophila Melanogaster, Ross Mckinney

Arts & Sciences Graduate Student Theses and Dissertations

Successful mating in diverse animal species often depends on ritualistic sequences of spatially and temporally coordinated behavioral elements. Yet, the sensory cues and neural circuits that mediate optimal mating display patterns are largely unknown. The courtship ritual in Drosophila melanogaster consists of a well-studied sequence of behavioral elements — including orienting, chasing, tapping, singing, and licking — that are known to depend on several sensory modalities, including both vision and chemosensation. However, the specific sensory inputs utilized by males to direct the spatial and temporal transitions between different elements of the courtship ritual are not well understood. In this thesis, …

Elucidation Of The Role Of S100a8/A9 And Neutrophils In Chronic Tuberculosis, Ninecia Scott

Arts & Sciences Graduate Student Theses and Dissertations

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is the number one killer due to a single infectious agent. Although, there is a vaccine against TB and antimicrobial treatments available, approximately 1.8 million people die each year. This underlines the importance of identifying and understanding mediators of TB pathogenesis to develop new diagnostics for early detection and therapies to treat individuals progressing to active disease. One of the cellular mediators that may play a role in TB pathogenesis are neutrophils. Neutrophils have been associated with active Tuberculosis (ATB); however, the role that neutrophils play within Mtb infection and disease is still …

Mechanism Of Activation Of Uvrd Helicase By A Processivity Factor Mutl, Yerdos Ordabayev

Arts & Sciences Graduate Student Theses and Dissertations

E. coli UvrD is a superfamily 1A helicase/translocase involved in DNA repair, recombination, and replication. I investigated the role of E. coli MutL, a regulatory protein involved in methyl-directed mismatch DNA repair, in the regulation of UvrD-catalyzed DNA unwinding. Using single molecule fluorescence resonance energy transfer (FRET) and single round stopped-flow DNA unwinding experiments I demonstrated that MutL can activate latent UvrD monomer helicase activity and also stimulate UvrD dimer helicase activity. Furthermore, using analytical ultracentrifugation experiments I determined that a single MutL dimer is sufficient to activate UvrD monomer helicase. DNA unwinding experiments with a series of DNA substrates …

Diverse Far-Red Light Utilization Strategies In Cyanobacteria And Algae, Benjamin Martin Wolf

Arts & Sciences Graduate Student Theses and Dissertations

In their natural environments, photosynthetic organisms are often exposed to widely varied light environments. Species adapted to shade light, often found growing in lower layers of photosynthetic biofilms, must survive on filtered light alone. Filtered light is highly enriched in far-red wavelengths, which are normally unavailable for photosynthetic energy production in most oxygenic phototrophs. To overcome light limitations in filtered light environments, some species of algae and cyanobacteria utilize specialized photosynthetic pigments and antenna systems to harvest these far-red wavelengths. By sampling the natural environment and using custom-built far-red light growth chambers, I have isolated several species of oxygenic phototrophs …

Mechanisms Of Nestmate Recognition Cue Production In The European Honey Bee, Apis Mellifera., Cassondra Leigh Vernier

Arts & Sciences Graduate Student Theses and Dissertations

Social insects are some of the world’s most ecologically successful animal groups, and their complex societies are considered one of the pinnacles of animal evolution. Since these organisms live in colonies composed of many individuals and stored resources, they are a target for intruders, such as parasites, predators and conspecific robbers. Therefore, many social insect species have evolved mechanisms for nest defense, including nestmate recognition, where guarding individuals at the entrance of the colony use cues on incoming individuals to determine whether they are nestmates or intruders. Although nestmate recognition is incredibly important for maintaining colony integrity and fitness, the …

Secretory Iga Enhances Gut B Cells Priming And Systemic Igg Responses Towards Commensals, You Zhou

Arts & Sciences Graduate Student Theses and Dissertations

IgA is the primary antibody response at mucosal surfaces and is reported to inhibit adaptive immune responses against gut bacteria. Here, we utilize an in vitro system to expand and screen IgA memory B cells for their ability to recognize gut bacteria in the context of secretory IgA (sIgA) deficiency in polymeric Ig receptor (Pigr–/–) mice. Contrary to the prevailing hypothesis that IgA provides an immune exclusionary function, we found that mice lacking sIgA showed decreased anti-bacterial IgA specificities as assessed using flow cytometry. IgA B cell responses against certain taxa such as those of order Bacteriodales showed greater dependence …

Cyanogenesis And The Genetics Of Local Adaptation In White Clover (Trifolium Repens L.), Sara Jeanes Wright

Arts & Sciences Graduate Student Theses and Dissertations

Geographically widespread species experience varied selection across their ranges, and adaptation to local environments plays a critical role in their ability to persist. Understanding the genetic basis of local adaptation is a longstanding goal in evolutionary biology and provides practical information for agriculture and conservation. However, the genetic architecture of local adaptation has been characterized in relatively few plant species, primarily those with short lifespans and high rates of self-fertilization. Moreover, for plants, chemical defenses are known to play an important role in adaptation, but the extent to which they contribute to local adaptation is less understood. This dissertation provides …

Investigating How Faculty Social Networks And Peer Influence Relate To Knowledge And Use Of Evidence-Based Teaching Practices, A. K. Lane, John Skvoretz, J. P. Ziker, Brian A. Couch, B. Earl, J. E. Lewis, J. D. Mcalpin, L. B. Prevost, S. E. Shadle, Marilyn Stains

School of Biological Sciences: Faculty Publications

Background: Calls for science education reform have been made for decades in the USA. The recent call to produce one million new science, technology, engineering, and math (STEM) graduates over 10 years highlights the need to employ evidence-based instructional practices (EBIPs) in undergraduate STEM classes to create engaging and effective learning environments. EBIPs are teaching strategies that have been empirically demonstrated to positively impact student learning, attitudes, and achievement in STEM disciplines. However, the mechanisms and processes by which faculty learn about and choose to implement EBIPs remain unclear. To explore this problem area, we used social network analysis …

Loss Of Developmental Diapause As Prerequisite For Social Evolution In Bees, Priscila Karla Ferreira Santos, Maria Cristina Arias, Karen M. Kapheim

Biology Faculty Publications

Diapause is a physiological arrest of development ahead of adverse environmental conditions and is a critical phase of the life cycle of many insects. In bees, diapause has been reported in species from all seven taxonomic families. However, they exhibit a variety of diapause strategies. These different strategies are of particular interest since shifts in the phase of the insect life cycle in which diapause occurs have been hypothesized to promote the evolution of sociality. Here we provide a comprehensive evaluation of this hypothesis with phylogenetic analysis and ancestral state reconstruction (ASR) of the ecological and evolutionary factors associated with …

Does A Carbonatite Deposit Influence Its Surrounding Ecosystem?, James M.C. Jones, Elizabeth A. Webb, Michael D.J. Lynch, Trevor C. Charles, Pedro M. Antunes, Frédérique C. Guinel

Biology Faculty Publications

Carbonatites are unusual alkaline rocks with diverse compositions. Although previous work has characterized the effects these rocks have on soils and plants, little is known about their impacts on local ecosystems. Using a deposit within the Great Lakes–St. Lawrence forest in northern Ontario, Canada, we investigated the effect of a carbonatite on soil chemistry and on the structure of plant and soil microbial communities. This was done using a vegetation survey conducted above and around the deposit, with corresponding soil samples collected for determining soil nutrient composition and for assessing microbial community structure using 16S/ITS Illumina Mi-Seq sequencing. In some …

Cancer Testis Antigen Promotes Triple Negative Breast Cancer Metastasis And Is Traceable In The Circulating Extracellular Vesicles, Anabarasu Kannan, Julie V. Philley, Kate L. Hertweck, Harrison Ndetan, Karan P. Singh, Subramaniam Sivakumar, Robert B. Wells, Ratna K. Vadlamudi, Santanu Dasgupta

Biology Faculty Publications and Presentations

Triple negative breast cancer (TNBC) has poor survival, exhibits rapid metastases, lacks targeted therapies and reliable prognostic markers. Here, we examined metastasis promoting role of cancer testis antigen SPANXB1 in TNBC and its utility as a therapeutic target and prognostic biomarker. Expression pattern of SPANXB1 was determined using matched primary cancer, lymph node metastatic tissues and circulating small extracellular vesicles (sEVs). cDNA microarray analysis of TNBC cells stably integrated with a metastasis suppressor SH3GL2 identifed SPANXB1 as a potential target gene. TNBC cells overexpressing SH3GL2 exhibited decreased levels of both SPANXB1 mRNA and protein. Silencing of SPANXB1 reduced migration, invasion …

The Effects Of Aging On Sleep Parameters In A Healthy, Melatonin-Competent Mouse Model, Jiffin K. Paulose, Chanung Wang, Bruce F. O'Hara, Vincent M. Cassone

Biology Faculty Publications

Background: Sleep disturbances are common maladies associated with human age. Sleep duration is decreased, sleep fragmentation is increased, and the timing of sleep onset and sleep offset is earlier. These disturbances have been associated with several neurodegenerative diseases. Mouse models for human sleep disturbances can be powerful due to the accessibility to neuroscientific and genetic approaches, but these are hampered by the fact that most mouse models employed in sleep research have spontaneous mutations in the biosynthetic pathway(s) regulating the rhythmic production of the pineal hormone melatonin, which has been implicated in human sleep.

Purpose and method: The present study …

The Vertebrate Tlr Supergene Family Evolved Dynamically By Gene Gain/Loss And Positive Selection Revealing A Host–Pathogen Arms Race In Birds, Imran Khan, Emanuel Maldonado, Liliana Silva, Daniela Almeida, Warren E. Johnson, Stephen James O'Brien, Guojie Zhang, Erich D. Jarvis, M. Thomas Gilbert, Agostinho Antunes

Biology Faculty Articles

The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) revealed differential gain/loss of 26 TLRs, including 6 (TLR3, TLR7, TLR8, TLR14, TLR21, and TLR22) that originated early in vertebrate evolution before the diversification of Agnatha and Gnathostomata. Subsequent dynamic gene gain/loss led to lineage-specific diversification with TLR repertoires ranging from 8 subfamilies in birds to 20 in fishes. Lineage-specific loss of TLR8-9 and TLR13 in birds and gains of TLR6 and TLR10-12 in mammals …