Digital Commons Network^™

Autophagy And Lipid Homeostasis In C. Elegans, Melissa J. Silvestrini

Dissertations, Theses, and Capstone Projects

The worldwide prevalence of obesity, particularly in developed nations, has become an epidemic in recent decades and the trend is continuing to rise. Moreover, the prevalence of obesity in children and adolescents is rising at an alarming rate. Obesity is associated with an increased risk of metabolic disorders including heart disease, insulin resistance, type 2 diabetes and nonalcoholic fatty liver disease. Therefore it is no surprise that lipid-related metabolic disorders have become a significant burden to our healthcare system. In recent years, the conserved cellular recycling process of autophagy has been linked to several lipid-related metabolic disorders, including insulin resistance, …

Examining Relationships Between Basic Emotion Perception And Musical Training In The Prosodic, Facial, And Lexical Channels Of Communication And In Music, Jamie Twaite

Dissertations, Theses, and Capstone Projects

Research has suggested that intensive musical training may result in transfer effects from musical to non-musical domains. There is considerable research on perceptual and cognitive transfer effects associated with music, but, comparatively, fewer studies examined relationships between musical training and emotion processing. Preliminary findings, though equivocal, suggested that musical training is associated with enhanced perception of emotional prosody, consistent with a growing body of research demonstrating relationships between music and speech. In addition, few studies directly examined the relationship between musical training and the perception of emotions expressed in music, and no studies directly evaluated this relationship in the facial …

Role Of Hnrnp A1 In The Regulation Of Hdm2 Gene Expression, Heriberto Moran

Dissertations, Theses, and Capstone Projects

hnRNP A1 is one of the most abundant and ubiquitously expressed member of hnRNPs (Heterogenous Nuclear Ribonucleoproteins) family of proteins that play multiple roles in gene expression by participating in major steps in the processing of nascent RNA transcripts 1. It is involved in mRNA biogenesis mechanisms such as the transcription, splicing, stability, export and translation of cellular and viral transcripts. The functions of hnRNP A1 extend to the processing of microRNAs, telomere maintenance and DNA repair 1. Our previous studies have shown that hnRNPA1 had reduced protein level and increased cytoplasmic accumulation in senescent human diploid fibroblasts 2,10. Our …

Molecular Analysis Of Ftsz-Ring Assembly In E. Coli Cytokinesis, Kuo-Hsiang Huang

Dissertations, Theses, and Capstone Projects

An essential first step in bacterial division is the assembly of a cytokinetic ring (Z-ring) formed by the tubulin-like FtsZ at midcell. The highly conserved core domain of FtsZ has been reported to mediate assembly of FtsZ polymers in vivo and in vitro. Species-specific differences in the FtsZ C-terminal domain such as the FtsZ CTV region and interactions with several modulatory proteins such as ZapC and ZapD, restricted to certain bacterial classes, also serve as key determinants of FtsZ protofilament bundling. Here, we characterize (i) the roles of the FtsZ CTV region in mediating both longitudinal and lateral interactions …

Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers

Dissertations, Theses, and Capstone Projects

Understanding the process of speciation is of central interest to evolutionary biologists. Speciation can be studied using a phylogeographic approach, by identifying regions that promote lineage divergence, addressing whether speciation has occurred with gene flow, and when extended to multiple taxa, addressing if the same patterns of speciation are shared across codistributed groups with different ecologies. Here I examine the comparative phylogeographic histories and population genomics of thirteen snake taxa that are widely distributed and co-occur across the arid southwest of North America. I first quantify the degree to which these species groups have a shared history of population divergence …

Models And Methods In Cultural And Social Evolution, Elliot G. Aguilar

Dissertations, Theses, and Capstone Projects

Chapter 1 The mathematical study of genealogies has yielded important insights in population biology, such as the ability to estimate the time to the most recent common ancestor (MRCA) of a sample of genetic sequences or of a group of individuals. Here we introduce a model of cultural genealogies that is a step toward answering similar questions for cultural traits. In our model individuals can inherit from a variable, potentially large number of ancestors, rather than from a fixed, small number of ancestors (one or two) as is typical of genetic evolution. We first show that, given a sample of …

Metabolic Profiling Of Genetically Modified Potato Periderm Tissues, Liqing Jin

Dissertations, Theses, and Capstone Projects

Potato tubers are protected from dehydration and pathogens by a covering peel (periderm) impregnated with suberin, a complex cross-linked biopolymer that contains both polyaliphatic and lignin-like aromatic domains. Current models describing the macromolecular structure of suberin assume that ferulic acid cross-links both domains as it may form carboxyl ester bonds with aliphatic monomers and non-ester radical-coupled bonds with phenolics. Ferulic acid also links by ester bonds to glycans and acts in cross-linking polysaccharides and lignin. Fatty alcohol/ω-hydroxyacid hydroxycinnamoyl transferase (FHT) is a BADH acyltransferase responsible for the synthesis of akyl-ferulates that is necessary for suberin biosynthesis. Periderm from FHT-RNAi …

The Role Of Individual Cognitive And Behavioral Ontogeny In Organization And Evolution Of Social Systems, Andrew G. Fulmer

Dissertations, Theses, and Capstone Projects

Exploration and explanation of the relationship between individual variation in behavior and the composition and adaptive success of social groups or populations are crucial problems in the fields of behavioral ecology, ethology, and comparative psychology. These questions have been the subject of a longstanding discussion at both the proximate and ultimate levels of inquiry. Adaptive mechanisms explaining social decision making, both in terms of affiliative and competitive partner choices, are at the center of such discussions. Inclusive fitness, kin-selection, handicap or prestige, risk seeking and risk avoiding strategies, pay-to-stay/reward principles, as well as other theories have been proposed and supported …

Metabolic Profiling And Polymer Formation Of Gene Silenced Potato Periderms, Qing Cai

Dissertations, Theses, and Capstone Projects

Suberin is a biopolyester constituent of specialized plant periderm tissues formed within the phellem cell walls. Suberin and waxes of the periderm layer act to prevent water diffusion, mechanical breakdown and pathogenic invasion in plants. Ferulic esters, ω-hydroxyacids and α,ω-fatty diacids are considered to be the most important linkage between aliphatic and aromatic suberin domains and also linked with cell-wall polysaccharides. The potato gene FHT (fatty ω- hydroxyacid/fatty alcohol hydroxycinnamoyl transferase) esterifies ferulic acid to suberin. Diminished levels of feruloyl transferase activity have been associated with lowered amounts of feruloyl esters of fatty acids in both suberin-associated waxes and suberin …

Computerized Classification Of Surface Spikes In Three-Dimensional Electron Microscopic Reconstructions Of Viruses, Younes Benkarroum

Dissertations, Theses, and Capstone Projects

The purpose of this research is to develop computer techniques for improved three-dimensional (3D) reconstruction of viruses from electron microscopic images of them and for the subsequent improved classification of the surface spikes in the resulting reconstruction. The broader impact of such work is the following.

Influenza is an infectious disease caused by rapidly-changing viruses that appear seasonally in the human population. New strains of influenza viruses appear every year, with the potential to cause a serious global pandemic. Two kinds of spikes – hemagglutinin (HA) and neuraminidase (NA) – decorate the surface of the virus particles and these proteins …

Tuning Into Toxins And Channels: The Characterizations Of Tv1 And A Human Cardiac Sodium Channel Voltage-Sensor Domain, Mohammed H. Bhuiyan

Dissertations, Theses, and Capstone Projects

In nature, peptide toxins are an abundant resource, produced both by marine and terrestrial organisms. A major target of these peptide toxins is the group of the highly important voltage-gated ion channels. Due to their high specificity and affinity, peptide toxins have been used for over a decade in discovery and characterization of voltage-gated ion channels. Although peptide toxins have been extensively characterized structurally, the structural characterization of eukaryotic voltage-gated sodium channels has seen much less progress, due to their large size and high hydrophobicity. Voltage-gated sodium channels play crucial roles in many physiological processes, and when these processes are …

The Regulation Of The Phosphatidate Phosphatase Gene Pah1 And Its Regulatory Role On Cell Homeostasis, Goldie Libby Sherr

Dissertations, Theses, and Capstone Projects

The Saccharomyces cerevisiae gene, PAH1, encodes a phosphatidate (PA) phosphatase that plays a fundamental role in lipid metabolism. PA phosphatases are key enzymes that catalyze the PA dephosphorylation reaction to form diacylglycerides, the first step in the synthesis of triacylglycerols. Pah1p, one of the main PA phosphatases in yeast, has not only emerged as a key player in lipid biosynthetic pathways, but also acts as an important regulator of nuclear membrane biogenesis, the transcriptional regulation of many inositol-sensitive upstream activating sequence (UAS_INO)containing genes needed for phospholipid synthesis, vacuole homeostasis, and lipid droplet formation. Due to its …

Adult Neurogenesis In Avian Auditory Cortex, Caudomedial Nidopallium (Ncm): Lateralization And Effects Of Statins, Shuk C. Tsoi

Dissertations, Theses, and Capstone Projects

In the first part of this paper, we investigated the basic relationship between learning, memory and adult neurogenesis using zebra finches. We found that in the auditory cortex, the left hemisphere had more new neurons than the right hemisphere. This lateralization was correlated with song learning and memory. In the second part, we used juvenile zebra finches as a model organism to study the effects of Lipitor on learning, memory and neurogenesis. We found that Lipitor impaired song learning and memory storage. Lipitor treatments also changed the morphology of new neurons and size of old neurons, suggesting statins may affect …

Therapeutic Targets For Alzheimer's Disease: Insights From In Vitro And In Vivo Models Of Inflammation, Magdalena J. Kiprowska

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive neuronal loss that over the years spreads from the hippocampus to the neural cortex and impairs memory and cognitive functions. At the cellular level AD is linked to the presence of β-amyloid plaques and neurofibrillary tangles but despite decades of research little is known about their contribution to neurodegeneration and whether they are a cause or rather a result of the disease. It is well established that proteasome activity is impaired in AD brains and some studies suggest that this could be one of the initial factors leading to development …

Phylogeny, Systematics And Biogeography Of Short-Tailed Opossums (Didelphidae: Monodelphis), Silvia E. Pavan

Dissertations, Theses, and Capstone Projects

Short-tailed opossums (genus Monodelphis) comprise the most species-rich genus of New World marsupials, with 25 currently recognized species. Monodelphis comprise small, terrestrial species collectively widespread in South America, which makes the group potentially informative about biogeographic processes that have shaped the continental fauna. The genus exhibits striking variation in several phenotypic characters, notably pelage coloration, behavior, and reproductive strategies. This diversity is unique among Neotropical marsupials, and makes the group particularly interesting to investigate the evolution and the adaptive significance of phenotypic trait variation. Despite this potential, missing knowledge on phylogeny and basic taxonomy precludes broader studies on evolution …

Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed

Dissertations, Theses, and Capstone Projects

Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and …

On The Screen, In The Mind: An Erp Investigation Into The Interaction Between Visuo-Spatial Information And Spatial Language During On-Line Processing, Emily Zane

Dissertations, Theses, and Capstone Projects

This project used Event-Related Potentials (ERPs) to explore neurophysiological brain responses to prepositional phrases involving concrete and abstract reference nouns (e.g., "plate" and "moment", respectively) after the presentation of objects with varying spatial features. Prepositional phrases were headed by in or on and were either matching (e.g., "in the plate/moment") or mismatching (e.g., "on the plate/moment"). Conjunction phrase matches and fillers were also presented. Before half of the concrete-phrase items, a photographic depiction of the reference noun was presented. In these photographs, objects were displayed in a way that was either more appropriate for in or for on. Similarly, before …

Circular Oligodeoxynucleotides (Coligos) As Chemically Synthesized, Promoter-Independent Small Rna Expression Vectors, Lodoe Lama

Dissertations, Theses, and Capstone Projects

Small RNAs (sRNA) such as microRNA (miRNA), small interfering RNA (siRNA), and other types of RNA have been found to play many important biological roles in regulation of different cellular process leading to their possible use as therapeutics. However, one of the biggest hurdles in exploiting these sRNAs in therapeutics has been the difficulty in delivering them safely and stably into human tissues. Many delivery approaches have been undertaken to deliver these sRNA, albeit with many shortcomings in terms of cost, stability, and side effects, necessitating the need for alternative approaches. We are exploring an entirely different approach for conveying …

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is …

Transition Issues In Educational Audiology, Rebecca Bareli

Dissertations, Theses, and Capstone Projects

Despite advancements in assistive technology for hearing loss (hearing aids, cochlear implants), children with hearing loss still face a host of issues throughout the educational process, particularly during transitional periods. This literature review examines the existing research discussing these issues, including transitions from childhood to adolescence, high school to college, and college to the workforce.

Mechanisms Of Immune Activation And Suppression By Parasitic Wasps Of Drosophila, Johnny R. Ramroop

Dissertations, Theses, and Capstone Projects

Drosophila melanogaster has served as an excellent model organism to study the molecular processes of innate immunity. Flies essentially lack adaptive immunity and the innate immune system is often divided into the humoral and cellular responses (Lemaitre and Hoffmann 2007). The humoral arm involves the production of antimicrobial peptides, secreted from the fat body, to combat bacterial and fungal infections. The cellular response involves the production of hemocytes (blood cells: crystal cells, plasmatocytes, and lamellocytes) in the larval lymph gland, in the sessile pools, and in circulation (Gold and Bruckner 2014). Microbial pathogens are phagocytosed by plasmatocytes whereas larger parasites …

Obesity Over The Life Course: Perspectives In Health And Mortality, Noura E. Insolera

Dissertations, Theses, and Capstone Projects

This dissertation seeks to examine obesity in different contexts throughout the life course. Through empirical analyses, separate stages of the life course are considered: namely childhood through adolescence, young adulthood, and adulthood. By using a life course perspective, it is possible to consider longitudinal and intergenerational approaches to these questions, which will update and inform the current debates surrounding obesity.

Beginning with children, the intergenerational transmission of diet disease knowledge, socioeconomic status, and child health behaviors are considered in their associations with the outcomes of child diet in 2002, and in turn their associations with child obesity in 2007. Information …

Reliability Of Clinical Evaluators Of Spasticity In Patients With Stroke, Tiffany Alvino, Shiney David, Chelsea Gendvil

Dissertations, Theses, and Capstone Projects

Spasticity is characterized by hyperexcitable stretch reflexes with amplitude increases in response to velocity dependent passive movement and resistance. Spasticity is the result of abnormal function of segmental and suprasegmental neuronal circuits. The objective of this study was to determine any positive correlation between three clinical evaluators of spasticity (i.e., the pendulum test, the patellar tendon tap test (PTT), and the Modified Ashworth scale) in their reliability to assess spasticity in people post-stroke. It was hypothesized that the use of force movement sensors along with surface electromyography increases the reliability of the standardized clinical tests. The results show that all …

Biosynthesis And Roles Of Virulence Conferring Cell Wall Associated Dimycocerosate Esters In Mycobacterium Marinum, Poornima Mohandas

Dissertations, Theses, and Capstone Projects

Mycobacterial species include a variety of obligate and opportunistic pathogens that cause several important diseases affecting mankind such as tuberculosis and leprosy. The most unique feature of these bacteria is their intricate cell wall that poses a permeability barrier to antibiotics and contributes to their pathogenicity and persistence within the host. The cell wall hosts several complex lipids such as dimycocerosate esters (DIMs), which are found in many clinically relevant pathogenic species of mycobacteria. DIMs have been implicated in the virulence of mycobacteria and play a major role in helping the bacteria evade host immune responses. It is therefore crucial …

Effect Of Cntf Derived Peptide, P021 On Cognition And Pathology In 3xtg-Ad Mouse Model Of Alzheimer's Disease, Narjes Baazaoui

Dissertations, Theses, and Capstone Projects

Studies described in this thesis deal with the preventive effects of a neurogenic/neurotropic peptidergic compound, P021, on neurogenesis and synaptic deficits, neurodegeneration, cognitive impairment, and Ab and tau pathologies in a 3xTg-AD mouse model of Alzheimer’s disease (AD).

Background: AD is a chronic progressive neurodegenerative disease. Its multifactorial nature and the heterogeneity make its treatment especially challenging. Although it is a major burden in society, at present there is no drug that can stop or slow down the progression of the disease. Currently, the only available treatments are symptomatic and for mild to severe stages. The development of a drug …

The Evolution Of The Viral Rna Sensor Oas1 In Old World Monkeys And Cetartiodactyls, Ian Fish

Dissertations, Theses, and Capstone Projects

Animals produce an array of sensors patrolling the intracellular environment poised to detect and respond to viral infection. The oligoadenylate synthetase family of enzymes comprises a crucial part of this innate immune response, directly signaling endonuclease activity responsible for inhibiting viral replication. Oligoadenylate synthetase 1 plays a vital role in animal susceptibility to pathogens including flaviviruses such as dengue, West Nile, and hepatitis c virus. This thesis includes a population level analysis of OAS1 diversity within macaque and baboon species followed by a broader survey of the gene in nineteen Old World monkeys. My research found that at the species …

Chamber-Specific Patterns Of Epicardium Formation In Zebrafish, Sana Khan

Dissertations, Theses, and Capstone Projects

The outer cardiac layer, the epicardium, coordinates the final steps of vertebrate heart development. This cardiac tissue arises from cells in the proepicardial organ (PEO) that forms around the base of the inflow tract. Its general location is conserved across species despite morphological differences. Cellular mechanisms of migration differ across species. Three strategies of PEO migration are described: 1) The floating cyst model - PEO cells released into the pericardial cavity are directed by fluid movements to migrate onto the myocardium; 2) Villi transfer - cardiac contractions may mediate multicellular PEO villi contact to the myocardium; and 3) Tissue bridge-mediated …

Messenger Rna Transport And Translation Regulated By The 3' Utrs Of Dendritic Mrnas And Abnormal Alternative Splicing Of Neuroligin1 In The Fmr1 Ko Mouse Hippocampus, Tianhui Zhu

Dissertations, Theses, and Capstone Projects

Fragile X Syndrome (FXS) is one of the most commonly inherited mental retardations. It is caused by the loss of functional fragile X mental retardation protein (FMRP). Loss of functional FMRP is the most widespread single-gene cause of autism. The most prominent phenotype of FXS patients is an IQ ranging from 20 to 70. FMRP is an RNA binding protein, widely expressed in almost all tissues and highly expressed in brain. As a RNA binding protein, 85-90 % of FMRP in the brain is associated with polyribosomes. Approximately 4 % of total mRNA is associated with FMRP, which functions in …

Lim Protein Ajuba Participates In The Repression Of Atr-Mediated Dna Damage Response In Human Cells, Sampada Kalan

Dissertations, Theses, and Capstone Projects

LIM proteins constitute a superfamily characterized by the presence of specialized domains called LIM. LIM domain is a unique double-zinc finger motif found in a variety of proteins and is mainly involved in protein-protein interactions. Previous work has implicated that members of the Zyxin subfamily of LIM proteins, namely TRIP6 and LPP are involved in the repression of the DNA damage response (DDR) at telomeres. We further explore if another member from this family has an influence on DDR prevention in the cells. Here, we describe a novel role for Ajuba, a Zyxin family LIM protein, in repressing inappropriate activation …

Role Of Bec-1/Beclin 1 And Autophagy Genes In C.Elegans Germline Cell Proliferation, Kristina Ames

Dissertations, Theses, and Capstone Projects

Autophagy is an evolutionary conserved process involved in the cellular adaptation to stress and basal levels of autophagy are crucial for cellular metabolism and homeostasis. Cellular recycling by autophagy is characterized by the formation of distinctive double-membrane vesicles (autophagosomes) that engulf unnecessary cytoplasmic components, such as organelles and long-lived proteins. Failure to remove protein aggregates and/or damaged organelles, via autophagy, has been implicated in various medical conditions such as liver disease, neurodegenerative diseases and cancer. Autophagy may suppress or promote cellular proliferation in tumors, depending on the type and metabolic state of the cell, where autophagy is generally believed to …