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Toxicogenomics Analysis Of Non-Model Transcriptomes Using Next-Generation Sequencing And Microarray, Arun Rawat

Dissertations

With the advent of next generation technologies like Roche/454 Life Sciences that require low cost and less time for sequencing will help in providing a workable draft of non-model species genomes. Availability of high throughput microarray technologies for gene expression profiling provides low-cost tools for investigation of highly-integrated responses to various stimuli. These advancements along with bioinformatics processing have led to an increasing number of non-model species having well-annotated transcriptomes. The project focuses on the life cycle of development, functional annotation, and utilization of genomic tools for the avian wildlife species to determine the molecular impacts of exposure to munitions …

Hsp70 And Hsp40 Functionally Interact With Soluble Mutant Huntingtin Oligomers In A Classic Atp-Dependent Reaction Cycle, Gregor P. Lotz, Justin Legleiter, Rebecca Aron, Emily M. Sontag, Shao-Yi Huang, Cheping Ng, Charles G. Glabe, Leslie M. Thompson, Paul J. Muchowski

Biological Sciences Faculty Research and Publications

Inclusion bodies of aggregated mutant huntingtin (htt) fragments are a neuropathological hallmark of Huntington disease (HD). The molecular chaperones Hsp70 and Hsp40 colocalize to inclusion bodies and are neuroprotective in HD animal models. How these chaperones suppress mutant htt toxicity is unclear but might involve direct effects on mutant htt misfolding and aggregation. Using size exclusion chromatography and atomic force microscopy, we found that mutant htt fragments assemble into soluble oligomeric species with a broad size distribution, some of which reacted with the conformation-specific antibody A11. Hsp70 associated with A11-reactive oligomers in an Hsp40- and ATP-dependent manner and inhibited their …

Regulation Of Biofilm And Antibiotic-Resistance By The Modulator Of Sara (Msa) In Staphylococcus Aureus, Antony Schwartz

Dissertations

Staphylococcus aureus is an important human pathogen that is the causative agent of life-threatening diseases such as endocarditis and osteomyelitis. The ability of S. aureus to thrive as a successful pathogen can be partially attributed to its ability to form biofilm. Biofilm is an extracellular polysaccharide, protein, and DNA-based slime layer that protects the bacterial community. The global regulator sarA is essential for biofilm formation. Since the modulator of sarA (msa) gene regulates several virulence factors and is required for the full expression of sarA, the capacity of the msa mutant to form a biofilm was examined. The mutation of …

Plasmacytoid Dendritic Cells Sense Skin Injury And Promote Wound Healing Through Type I Interferons, Josh D. Gregorio

Dissertations and Theses (Open Access)

Plasmacytoid dendritic cells (pDCs) are a rare population of circulating cells, which selectively express intracellular Toll-like receptors (TLR)-7 and TLR-9 and have the capacity to produce large amounts of type I IFNs (IFN-a/b) in response to viruses or host derived nucleic acid containing complexes. pDCs are normally absent in skin but accumulate in the skin of psoriasis patients where their chronic activation to produce IFN-a/b drives the disease formation. Whether pDCs and their activation to produce IFN-a/b play a functional role in healthy skin is unknown. Here we show that pDCs are rapidly and transiently recruited into healthy human and …

14-3-3sigma Negatively Regulates The Stability And Subcellular Localization Of Cop1, Chun-Hui Su

Dissertations and Theses (Open Access)

Mammalian constitutive photomorphogenic 1 (COP1), a p53 E3 ubiquitin ligase, is a key negative regulator for p53. DNA damage leads to the translocation of COP1 to the cytoplasm, but the underlying mechanism remains unknown. We discovered that 14-3-3σ controlled COP1 subcellular localization and protein stability. Investigation of the underlying mechanism suggested that, upon DNA damage, 14-3-3σ bound to phosphorylated COP1 at S387, resulting in COP1 translocation to the cytoplasm and cytoplasmic COP1 ubiquitination and proteasomal degradation. 14-3-3σ targeted COP1 for degradation to prevent COP1-mediated p53 degradation, p53 ubiquitination, and p53 transcription repression. COP1 expression promoted cell proliferation, cell transformation, and …

Effect Of Stress On Mucin Expression In The Gastrointestinal Tract Of Mice., Bupe Martha Habiyambere

Electronic Theses and Dissertations

This study investigated the effects of chronic stress on mucin expression in the GIT of mice. Sixteen ICR male mice were randomly divided into treated and control animals. Restraint stress was applied to the treated group for 21 days. Body weight (BW) changes and feed consumed (FC) were regularly recorded. After 21 days mice were euthanized and blood, GIT mucosa, and GIT sections were collected. Serum corticosterone levels were determined. The GIT sections were fixed, paraffin embedded, sectioned, and stained with AB-PAS to visualize goblet cells. Mucin expression was determined using qPCR. As expected stressed mice showed higher corticosterone than …

Structure And Expression Of Two Nuclear Receptor Genes In Marsupials: Insights Into The Evolution Of The Antisense Overlap Between The Α-Thyroid Hormone Receptor And Rev-Erbα, Brandon C. Rindfleisch, M. Scott Brown, John L. Vandeberg, Stephen Munroe

Biological Sciences Faculty Research and Publications

Background: Alternative processing of α-thyroid hormone receptor (TRα, NR1A1) mRNAs gives rise to two functionally antagonistic nuclear receptors: TRα1, the α-type receptor, and TRα2, a non-hormone binding variant that is found only in mammals. TRα2 shares an unusual antisense coding overlap with mRNA for Rev-erbα (NR1D1), another nuclear receptor protein. In this study we examine the structure and expression of these genes in the gray short-tailed opossum, Monodelphis domestica, in comparison with that of eutherian mammals and three other marsupial species, Didelphis virginiana, Potorous tridactylus and Macropus eugenii, in order to understand the evolution and regulatory …

Environmental Influence On Brain, Behavior, And Gene Expression In Drosophila, Xia Wang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Brain development and behavior are sensitive to environmental stimuli. To gain an understanding of how and to what extent environmental variations, particularly with regard to thermal stress and sensory input, affect brain development, function, and genomic activity, in this dissertation, three interrelated studies were conducted in Drosophila melanogaster.

The first study examined the effects of ecologically-relevant hyperthermia stress on development of the Drosophila mushroom body (MB), a conserved sensory integration and associative center in the insect brain. A daily hyperthermic episode throughout larval and pupal development was shown to severely disrupt MB anatomy by reducing intrinsic Kenyon cell neuron …

Physiological Implications Of Natural Versus Induced Arousal From Torpor, Jenifer C. Utz

UNLV Theses, Dissertations, Professional Papers, and Capstones

During the hibernation season, animals oscillate between periods of torpor and periods of interbout arousal (IBA). During torpor, body temperature is often near 0° C and metabolism is severely depressed. Oxygen consumption, a proxy for aerobic metabolism, may fall to 1% of active values. Many physiological processes including cardiovascular, respiratory, and cellular functions nearly cease. During the IBA, euthermic body temperature is restored and most systemic and cellular processes function at fully active levels. The transition period between these two physiologically dissimilar states is called arousal.

The rate of rewarming (RRW) during arousal was previously expected to progressively increase until …

Microsatellite Development, Population Structure And Demographic Histories For Two Species Of Amazonian Peacock Bass Cichla Temensis And Cichla Monoculus (Perciformes: Cichlidae)., Jason C. Macrander

School of Biological Sciences: Dissertations, Theses, and Student Research

The Neotropics of South America represent one of the most diverse assemblages of freshwater organisms in the world. The geologic and ecological changes that have occurred throughout the Amazon and Orinoco River basins have resulted in the two most diverse rivers in the world producing very heterogeneous environments potentially influencing current population structure of Neotropical species. To investigate specific ecological and geological events influencing populations in these regions, I explore population structure and demographic histories of two species from the genus Cichla with wide distributions among the Amazon and Orinoco. First, I describe the methods used to isolate and characterize …

The Spatial Ecology Of Galapagos Tortoises And New Mexico's Reptiles, Jacek Tomasz Giermakowski

Biology ETDs

The analysis of spatial processes and spatial heterogeneity is an important part of ecology because distribution of organisms in space partly defines ecology as a discipline. In addition, advances in analysis of DNA, geographical computing and the availability of vast amounts of environmental data obtained by satellites provide new opportunities for studying ecology at different spatial and phylogenetic scales. My research takes advantage of information gathered by satellites and adds modeling and data collected on the distribution of different reptiles to examine processes at various spatial and temporal scales. In Chapter 1 I describe how juvenile Galapagos tortoises change their …

Biogeography Of Alien Vertebrates In The Galapagos Islands: Patterns, Processes, And Conservation Implications, Reese Brand Phillips

Biology ETDs

Alien species are one of the principal threats to global biodiversity. Insular ecosystems have proven exceptionally susceptible to invasion by aliens and vulnerable to their negative effects. Some of the most destructive alien species are vertebrates, in part due to their having been introduced to islands worldwide. Rodents (Rattus spp. and Mus musculus) are among the most widespread and devastating invasive species for insular flora and fauna. In this research I investigate the biogeographic patterns and processes of alien vertebrates in the Galapagos Islands, focusing on the mechanisms that influence their dispersal and colonization within the archipelago. In the first …

Characterization Of Transgenic Plum Lines Expressing Gastrodia Antifungal Protein (Gafp)-1, Hetalben Kalariya

All Theses

The Gastrodia antifungal protein (GAFP-1) is a mannose-binding lectin originating from the Asiatic orchid Gastrodia elata. It has potential for conferring resistance to fungal and non-fungal pathogens in other plants which is currently being investigated. The goals of this research project were to determine (i) the potential movement of GAFP-1 protein from transgenic rootstocks into the non-transgenic scion of chimeric-grafted trees (ii) the levels of GAFP-1 protein in lines of the cultivar Bluebyrd expressing the gene gafp-1 under the control of the polyubiquitin promoter bul409, and (iii) the susceptibility of selected lines to the root pathogens Phytophthora cinnamomi Rands and …

Historical Biogeography Of Velvet Ants (Hymenoptera: Mutillidae) In The North American Deserts And Arid Lands, Joseph S. Wilson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For centuries, scientists have been intrigued by the high amount of biodiversity that is found in the deserts of North America. Recently, several studies have investigated the causes of the high diversity found in desert-dwelling mammals, reptiles, and amphibians. These studies have found that many of these organisms seem to have diversified in response to the same historical events. Little work has been done, however, on diverse desert-dwelling insect groups. In this dissertation, I investigate the patterns of genetic diversity in four groups of nocturnal wasps called velvet ants. I compare the patterns of genetic diversity to the historical events …

Muscle Receptor Organs In The Crayfish Abdomen: A Student Laboratory Exercise In Proprioception, Bonnie Leksrisawat, Ann S. Cooper, Allison B. Gilberts, Robin L. Cooper

Biology Faculty Publications

The primary purpose of this experiment is to demonstrate primary sensory neurons conveying information of joint movements and positions as proprioceptive information for an animal. An additional objective of this experiment is to learn anatomy of the preparation by staining, dissection and viewing of neurons and sensory structures under a dissecting microscope. This is performed by using basic neurophysiological equipment to record the electrical activity from a joint receptor organ and staining techniques. The muscle receptor organ (MRO) system in the crayfish is analogous to the intrafusal muscle spindle in mammals, which aids in serving as a comparative model that …

Physiological Recordings Of High And Low Output Nmjs On The Crayfish Leg Extensor Muscle, Wenhui Wu, Robin L. Cooper

Biology Faculty Publications

We explain in detail how to expose and conduct electrophysiological recordings of synaptic responses for high (phasic) and low (tonic) output motor neurons innervating the extensor muscle in the walking leg of a crayfish. Distinct differences are present in the physiology and morphology of the phasic and tonic nerve terminals. The tonic axon contains many more mitochondria, enabling it to take a vital stain more intensely than the phasic axon. The tonic terminals have varicosities, and the phasic terminal is filiform. The tonic terminals are low in synaptic efficacy but show dramatic facilitated responses. In contrast, the phasic terminals are …

Micrornas Reveal The Interrelationships Of Hagfish, Lampreys, And Gnathostomes And The Nature Of The Ancestral Vertebrate, Alysha M. Heimberg, Richard Cowper-Sal{Middle Dot}Lari, Marie Semon, Philip C. J. Donoghue, Kevin J. Peterson

Dartmouth Scholarship

Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more …

Diatoms As Indicators Of Water-Level Change In Freshwater Lakes, Julie A. Wolin, Jeffrey R. Stone

Biological, Geological, and Environmental Faculty Publications

Water-level changes result from a variety of geological, biological, and/or climatic processes. Many of these changes occur over long periods; others may be rapid or result from catastrophic events. In aquatic environments, diatoms are highly sensitive indicator organisms and their microfossils, deposited in lake sediments, can be used to infer environmental changes (Smol, 2008). Unambiguous diatom signals can be reconstructed from lakes isolated from marine or brackish waters (e.g. Fritz et al., this volume; Horton & Sawai, this volume). However, in freshwater systems lake-level changes are often recorded as increases in planktonic (free-floating) diatoms – although as discussed below, interpretation …

Using Critical-Thinking Skills To Substantiate Or Challenge Controversial Claims Endorsing A Myriad Of Weight-Loss Products, Teresa F. Degolier

Biological Sciences Faculty Publications

This exercise engages students in critically evaluating weight-loss products and programs. Specific objectives are to investigate, analyze, and substantiate claims made by the weight-loss industry and interpret how these claims may be fraudulent, misleading, or perhaps even truthful.

Hidden Consequences Of Living In A Wormy World: Nematode-Induced Immune Suppression Facilitates Tuberculosis Invasion In African Buffalo, Vanessa O. Ezenwa, Rampal S. Etienne, Gordon Luikart

Biological Sciences Faculty Publications

Most hosts are infected with multiple parasites, and responses of the immune system to co occurring parasites may influence disease spread. Helminth infection can bias the host immune response toward a T-helper type 2 Th2) over a type 1 Th1) response, impairing the host's ability to control concurrent intracellular microparasite infections and potentially modifying disease dynamics. In humans, immune-mediated interactions between helminths and microparasites can alter host susceptibility to diseases such as HIV, tuberculosis TB), and malaria. However, the extent to which similar processes operate in natural animal populations and influence disease spread remains unknown. We used cross-sectional, experimental, and …

Hidden Consequences Of Living In A Wormy World: Nematode‐Induced Immune Suppression Facilitates Tuberculosis Invasion In African Buffalo, Vanessa O. Ezenwa, Rampal S. Etienne, Gordon Luikart, Albano Beja-Pereira, Anna E. Jolles

Biological Sciences Faculty Publications

Most hosts are infected with multiple parasites, and responses of the immune system to co-occurring parasites may influence disease spread. Helminth infection can bias the host immune response toward a T-helper type 2 (Th2) over a type 1 (Th1) response, impairing the host’s ability to control concurrent intracellular microparasite infections and potentially modifying disease dynamics. In humans, immune-mediated interactions between helminths and microparasites can alter host susceptibility to diseases such as HIV, tuberculosis (TB), and malaria. However, the extent to which similar processes operate in natural animal populations and influence disease spread remains unknown.We used cross-sectional, experimental, and genetic studies …

The Role Of Caspases In Alzheimer's Disease; Potential Novel Therapeutic Opportunities, Troy T. Rohn

Biology Faculty Publications and Presentations

Although apoptosis plays a critical role in molding the CNS into its final appearance and function, inappropriate activation of this pathway in the aging brain may contribute to neurodegeneration. In Alzheimer’s disease (AD), an overwhelming body of evidence supports the activation of apoptosis in general, and caspases specifically as an early event that may not only contribute to neurodegeneration but also promote the underlying pathology associated with this disease. Therefore, caspase inhibitors may provide an effective strategy for treating AD. However, despite the compelling evidence indicating a role for caspases in disease progression, chronic treatment with caspase inhibitors in animal …

The Mathematics Of Animal Behavior: An Interdisciplinary Dialogue, Shandelle M. Henson, James L. Hayward

Faculty Publications

No abstract provided.

Non-Native Salmonids Affect Amphibian Occupancy At Multiple Spatial Scales, David S. Pilliod, Blake R. Hossack, Peter F. Bahls, Evelyn L. Bull, Paul Stephen Corn, Grant Hokit, Bryce A. Maxell, James C. Munger, Aimee Wyrick

Biology Faculty Publications and Presentations

Aim The introduction of non-native species into aquatic environments has been linked with local extinctions and altered distributions of native species. We investigated the effect of non-native salmonids on the occupancy of two native amphibians, the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), across three spatial scales: water bodies, small catchments and large catchments.

Location Mountain lakes at ≥ 1500 m elevation were surveyed across the northern Rocky Mountains, USA.

Methods We surveyed 2267 water bodies for amphibian occupancy (based on evidence of reproduction) and fish presence between 1986 and 2002 and modelled …

Effects Of Flooding On Photosynthesis And Root Respiration In Saltcedar (Tamarix Ramosissima), An Invasive Riparian Shrub, Kristen Polacik

Master's Theses or Doctor of Nursing Practice

The introduced shrub Tamarix ramosissima Lebed. invades riparian zones, but loses competitiveness under flooding. This was tested in Tamarix ramosissima by examining responses to flooding by soil type in a greenhouse setting. A field study examined responses of Tamarix ramosissima and other species to natural flooding. Leaf level photosynthesis rates, stomatal conductance, transpiration, and root alcohol dehydrogenase (ADH) activity were measured weekly to assess oxygen stress. In the field, stomatal conductance, leaf water potential, transpiration, canopy cover, and δ13C were measured as responses to soil water potential, soil moisture, Julian date, relative humidity, and water depth. In the greenhouse study, …

Genetic Analysis Of Vancomycin-Resistant Gram-Positive Cocci Isolated From Wild Songbirds, Shingo Ishihara

Master's Theses or Doctor of Nursing Practice

The antibiotic vancomycin was developed by Eli Lilly in the 1950s in response to the growing number of Staphylococcus aureus infections that were resistant to penicillin. Vancomycin was not widely used at the time because of its high toxicity. However, use of vancomycin in the United States has increased dramatically since the 1980s because of the emergence of methicillin resistant Staphylococcus aureus (MRSA) and Enterococcus species. There are three known mechanisms for vancomycin resistance: 1) target site modification by van genes, 2) biofilm formation, and 3) bacterial cell wall thickening. Of these mechanisms, target site modification is the most common. …

Genome Dynamics Are Influenced By Food Source In Allogromia Laticollaris Strain Csh (Foraminifera), Laura Wegener Parfrey, Laura A. Katz

Biological Sciences: Faculty Publications

Across the eukaryotic tree of life, genomes vary within populations and within individuals during their life cycle. Understanding intraspecific genome variation in diverse eukaryotes is key to elucidating the factors that underlie this variation. Here, we characterize genome dynamics during the life cycle of Allogromia laticollaris strain CSH, a member of the Foraminifera, using fluorescence microscopy and reveal extensive variation in nuclear size and DNA content. Both nuclear size and DNA content are tightly correlated across a 700-fold range in cell volume. In contrast to models in yeast where nuclear size is determined solely by cell size, the relationship in …

Neural Activity Patterns In Response To Interspecific And Intraspecific Variation In Mating Calls In The Túngara Frog, Mukta Chakraborty, Lisa A. Mangiamele, Sabrina S. Burmeister

Biological Sciences: Faculty Publications

Background: During mate choice, individuals must classify potential mates according to species identity and relative attractiveness. In many species, females do so by evaluating variation in the signals produced by males. Male túngara frogs (Physalaemus pustulosus) can produce single note calls (whines) and multi-note calls (whine-chucks). While the whine alone is sufficient for species recognition, females greatly prefer the whine-chuck when given a choice. Methodology/Principal Findings: To better understand how the brain responds to variation in male mating signals, we mapped neural activity patterns evoked by interspecific and intraspecific variation in mating calls in túngara frogs by measuring expression of …

Invasive Honeysuckle Eradication Reduces Tick-Borne Disease Risk By Altering Host Dynamics, Brian Allan, Humberto Dutra, Lisa Goessling, Kirk Barnett, Jonathan Chase, Robert Marquis, Genevieve Pang, Gregory Storch, Robert Thach, John Orrock

Biology Department Faculty Works

Despite the ubiquity of invasive organisms and their often deleterious effects on native flora and fauna, the consequences of biological invasions for human health and the ecological mechanisms through which they occur are rarely considered. Here we demonstrate that a widespread invasive shrub in North America, Amur honeysuckle (Lonicera maackii), increases human risk of exposure to ehrlichiosis, an emerging infectious disease caused by bacterial pathogens transmitted by the lone star tick (Amblyomma americanum). Using large-scale observational surveys in natural areas across the St. Louis, Missouri region, we found that white-tailed deer (Odocoileus virginianus), a preeminent tick host and pathogen reservoir, …

Dynamic Evolution Of Precise Regulatory Encodings Creates The Clustered Site Signature Of Enhancers, Justin Crocker, Nathan Potter, Albert Erives

Dartmouth Scholarship

Concentration gradients of morphogenic proteins pattern the embryonic axes of Drosophila by activating different genes at different concentrations. The neurogenic ectoderm enhancers (NEEs) activate different genes at different threshold levels of the Dorsal (Dl) morphogen, which patterns the dorsal/ventral axis. NEEs share a unique arrangement of highly constrained DNA-binding sites for Dl, Twist (Twi), Snail (Sna) and Suppressor of Hairless (Su(H)), and encode the threshold variable in the precise length of DNA that separates one well-defined Dl element from a Twi element. However, NEEs also possess dense clusters of variant Dl sites. Here, we show that these increasingly variant sites …