Life Sciences Commons^™

Musical Regularity And Rhythmic Patterns: A Quantitative Analysis Of Birdsong Structure, Eathan Ezra Janney

Dissertations, Theses, and Capstone Projects

Birdsong is a complex, learned behavior that, like music, has meaningful units at multiple timescales. Birds perform by constructing extended presentations of their phrase repertoire. Each bird's repertoire is built from small units, such as syllables, or groups of syllables with characteristic pitch, rhythm, and timbre. Like a musician each bird has its unique structure of performance that communicates its individual identity. Also contained within a bird's performance, is information about its group identity and species identity. Like a musician's performance, a bird's singing affects the behavioral state of listeners'birds perform to attract mates and defend territory.

Subjectively, many can …

Systematic Studies Of Elaphoglossum Section Polytrichia (Dryopteridaceae), Fernando Bittencourt De Matos

Dissertations, Theses, and Capstone Projects

Elaphoglossum is the largest genus of the largest family of ferns, the Dryopteridaceae. It has over 600 species distributed in the temperate and tropical regions of the world, but it is especially diverse in the Neotropics, where ca. 80% of the species occur. Morphologically, the genus is usually characterized by simple entire leaves, free veins, acrostichoid sori, and phyllopodia. One of the major clades within Elaphoglossum is the "subulate-scaled clade," which includes all species with subulate scales on the leaves. These scales are often patent and enrolled lengthwise, imparting a bristly or shaggy appearance to the plants. Previous studies have …

Population Genomics Of White-Footed Mice (Peromyscus Leucopus) In New York City, Stephen Edward Harris

Dissertations, Theses, and Capstone Projects

Urbanization significantly alters natural ecosystems. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC's forest fragments, and isolated populations may adapt in response to novel urban ecosystems. Using pooled transcriptome-wide RNAseq data, individually barcoded transcriptome-wide RNAseq data, and genome-wide RADseq data, I found genetic differentiation between urban and rural P. leucopus populations and evidence suggestive of local adaptation. I compared genome and transcriptome-wide SNP data in P. leucopus from relatively large urban …

Cultural Evolution In Natural Populations: A Quantitative Bioacoustic Analysis, Chenghui Ju

Dissertations, Theses, and Capstone Projects

Bird song is a powerful model system in behavioral biology, especially for learning and cultural evolution. Understanding the origins and maintenance of vocal diversity in nature is fundamentally important to acoustic biology. Here, we propose a large-scale, integrative population analysis of nearly 2000 songs of the house finch (Haemorhous mexicanus) (190 individuals) collected in western Long Island of New York during an interval of 37 years (between 1975 and 2012) to explore cultural change of bird songs. Generally, I have three aims in this study. In the chapter 1, to facilitate acoustic analysis for field recordings with ambient noise, of …

The Ecology Of Winter Flounder From An Otolith Perspective, George William Jackman

Dissertations, Theses, and Capstone Projects

In this dissertation, sagittal otoliths were used as a lens to examine latent life history patterns in winter flounder (Pseudopleuronectes americanus) and also as a means of interpreting the species' relationship to their abiotic and biotic environment. Otoliths provide a unique and powerful perspective into the lives of the telost fishes, because they permanently record the spatial and temporal histories through sequential growth patterns from conception to capture. The patterns of growth and dormancy in the otolith are regulated by endogenous and exogenous rhythms, and as the otolith grows, trace elements are absorbed from the ambient environment and …

Systematics And Evolution Of The Ronnbergia Alliance (Bromeliaceae): History Of Disjunct Diversification In Three Biodiversity Hotspots Of The Neotropics, Julian Andres Aguirre Santoro

Dissertations, Theses, and Capstone Projects

The systematics, biogeography and evolution of the 'Ronnbergia Alliance,' a nested lineage within the Core Bromelioideae, were investigated. In the first chapter, the phylogenetic relationships of the Ronnbergia Alliance were reconstructed using three chloroplast and three nuclear DNA sequence markers in combination with a wide species sampling across the Core Bromelioideae and a nearly complete species-level sampling of the five species complexes that likely comprise the Ronnbergia Alliance. The analysis indicates that the Ronnbergia Alliance is a robust monophyletic group sister to the remaining Core Bromelioideae, and it is composed by species of the polyphyletic genera Aechmea, Hohenbergia and Ronnbergia. …

Pseudomonas Bacteriophage Phi6 As A Model For Virus Emergence, Brian Elwood Ford

Dissertations, Theses, and Capstone Projects

The Pseudomonas bacteriophage Φ6 has a long and well-established history as a model organism. Here we describe a set of experiments to extend this model system to concepts previously unclaimed. Chapter 1 presents a brief background of the ecology of viruses that infect microorganisms. Chapter 2 examines genetic mutations allowing for host range expansion. Chapter 3 presents a novel paired strain assay to study how a non genetic host-acquired factor affects fitness of these enveloped viruses on subsequent hosts. Chapter 4 is an extension of this system to include how the bacteria host is affected in virus-host coevolution.

Incipient Speciation In Freshwater Fish Species From Two Isolated Watersheds, Paula Gore Miller

Dissertations, Theses, and Capstone Projects

The process of speciation occurs as a result of restricted gene flow between segments of an interbreeding population occupying different geographic areas. This separation may result in isolated populations which undergo genetic and phenotypic changes. The Wisconsin glacial period, which ended approximately 17,500 years ago, dramatically altered the geography of North America. The glacier covered almost the entire North America as it advanced. Areas that were not covered with ice provided suitable habitats (refugia) for relict species that were previously widespread in the northern section of the continent. As the ice sheet retreated, animals and plants were able to return …

Mechanisms Of Vocal Coordination In Zebra Finches, Jonathan I. Benichov

Dissertations, Theses, and Capstone Projects

Social animals frequently emit communication calls. Although these calls are often innate in their acoustic structure, they can be used adaptably to coordinate behavior with other individuals. It is not known, however, what each animal needs to learn in order to achieve and maintain synchronized call patterns with others. To study this process, we have developed a vocal robot that can be programed to generate call patterns or to sense a bird's contact (short) calls and respond with precisely timed call answers. By varying the robot's vocal behavior, including call timing and rhythm, we tested how interacting zebra finches adapt …

Matrix Stiffness Regulates Glial Cell Morphology And Differentiation, Mateusz M. Urbanski

Dissertations, Theses, and Capstone Projects

Studies from our laboratory have shown that inhibition of non-muscle myosin II (NMII) activity has opposite effects on the formation of myelin by oligodendrocytes (OL), the myelinating glia of the central nervous system (CNS) and Schwann cells (SC), which perform the same function in the peripheral nervous system (PNS). The decrease of NMII activity in SC impairs their ability to establish polarity and myelinate, while its inhibition in OL enhances process branching and increases the amount of myelin formed in vitro an in vivo. A growing number of studies have shown that NMII also plays a role in the ability …

Diversity And Phylogeography Of Anurans Of The Highlands Of Ethiopia, Xenia Freilich

Dissertations, Theses, and Capstone Projects

Located in Eastern Africa, Ethiopia is a country of unique geological features, among them the largest continuous Afro-alpine zone in Africa and the Great Rift Valley (GRV). The GRV formation began ~20 mya; it is a fault system that splits the central Ethiopian dome in two separate highland systems (Baker et al., 1972, Chorowicz, 2005). In spite of the general assumption that the GRV has played a major role in shaping the biodiversity of the country, its influence has not been fully investigated, as only a handful of studies have addressed its impact on the phylogeographic and evolutionary history of …

Climate, Resource Phenology, And Demographic Population Structure Impacts On Songbird Habitat Quality, Ashley Ozelski

Dissertations, Theses, and Capstone Projects

Monitoring bird populations becomes more complex as climate change alters species' relationships with their habitats. The presence of a species does not necessarily indicate a thriving population; in fact, we expect to see changes in demography and nest success before extinction at a site. Here, I first model aspects of demography as a proxy for habitat quality across a large portion of a species' range, using land cover and climate predictors. I show a gradient of high to low habitat quality from north to south within the range for the Yellow Warbler (Setophaga petechia), with summer temperature and …

The Role Of The Vta Nmda Receptors, Vta Da Cells And Vta Terminal Regions In Reward-Related Learning, Karen Kest

Dissertations, Theses, and Capstone Projects

Reward-related learning occurs when an initially neutral stimulus acquires the capacity to elicit responses similar to an unconditioned stimulus (US) with which it is associated, in which case the stimulus now functions as a conditioned stimulus (CS). The mechanisms whereby stimuli come to function as CSs are not fully understood and comprise the theme of this dissertation. We have previously proposed that coincident signals from an unconditioned and the eventual conditioned stimulus (US and CS) signals on dopamine (DA) cells of the ventral tegmental area (VTA) leads to strengthening of CS synapses, allowing the CS to acquire the ability to …

Phylogeography Of Southeast Asian Flying Foxes (Chiroptera: Pteropodidae: Pteropus), Susan Man Shu Tsang

Dissertations, Theses, and Capstone Projects

Flying foxes (Pteropus) are a genus of Old World fruit bats that are important seed dispersers and pollinators for plants native to the 200,000+ islands in Southeast Asia, yet they are some of the most poorly known bats in the world. They comprise some of the largest known bat species, and are morphologically relatively conserved on the genus level. Pteropus is the most species-rich genus within Pteropodidae, though the origin for this diversity remains incompletely understood. In Chapter 1, I discuss the importance of Pteropus to the ecosystem and as reservoir hosts. In Chapter 2, a molecular phylogeny is presented …

Testing Visual Ecology Hypotheses In Avian Brood Parasite-Host Systems: The Role Of Uv-Light Perception And Egg-Nest Contrast In Foreign Egg Rejection, Zachary Aidala

Dissertations, Theses, and Capstone Projects

Color signals are highly important features of animal communication systems, particularly among birds, which possess exquisitely complex visual perception systems. Birds possess tetrachromatic vision, and some species are sensitive to ultraviolet (UV) wavelengths. Because human and avian visual systems dramatically differ (i.e. humans are not sensitive to UV wavelengths), biologically relevant sensory models are necessary to accurately assess the function of avian color signals. In this dissertation, I primarily use brood parasite-host interactions as a model for studying the behavioral function of avian-perceivable visual stimuli. In Chapter 1, I review the importance of employing biologically relevant sensory-perceptual visual models when …

Control Of Cell Cycle Progression By Mtor, Amrita Chatterjee

Dissertations, Theses, and Capstone Projects

Over the past few years it has become apparent that cancer cells require the activation of a set of intra-cellular signals that promote cell cycle progression and survival. One of the most common survival signals activated in human cancers is mediated by mTOR -the mammalian target of rapamycin. mTOR is a critical nutrient and energy sensor in cells that lets the cell know that there is sufficient material available for a cell to double its mass and divide. mTOR causes the phosphorylation of downstream targets ribosomal subunit S6 kinase and eukaryotic initiation factor 4E (eIF4E) binding protein-1 (4E-BP1), which promotes …

Nuclear Pore Protein Nup211 Is Essential For Cell Cycle Progression And Cell Shape Maintenance In Fission Yeast, Ayisha R. Sookdeo

Dissertations, Theses, and Capstone Projects

The nuclear pore complexes (NPCs) are large multi-protein channels that traverse the nuclear envelope and mediate nucleo-cytoplasmic transport. Proteomic studies have revealed that NPCs are composed of about thirty different proteins called nucleoporins. I explored a particular nucleoporin, Nup211, in fission yeast. nup211 is an essential gene; its deletion is lethal and causes morphological defects. In this study, I characterized the cell morphological defects caused by the down-regulation of Nup211 and found that restoring the N-terminal domain of Nup211 was sufficient to rescue the lethal phenotype and partially suppress the morphological defects. Additionally, I investigated the role Nup211 plays in …

Tcr Alpha Lcr And Non-Lcr Cis-Elements Contributing To Tissue Specific Expression Of The Tcr Alpha Gene In Thymic And Peripheral T Cells, Martina Kucerova-Levisohn

Dissertations, Theses, and Capstone Projects

Orchestrated expression of multiple genes residing in the complex TCRα/δ/Dad1 locus requires tight control from multiple cis-acting elements. The TCRα locus control region (LCR), is positioned between TCRα and Dad1 gene, and has been implicated in the differential expression of both genes. In this study, we focus our work on the hypersensitive site (HS)1 prime (HS1'), located 3' of the classical Eα enhancer, within the TCRα LCR. We investigated its non- redundant role in TCRα expression in thymic and peripheral T cells as assayed by in vivo and in vitro studies. Furthermore, formation of HS1' in both lymphoid and …

Population Genomic Inference Of Ecology, Conservation, Evolution, And Demographic History Of Atlantic Seahorses And Pipefishes (Syngnathidae), Joel Thomas Boehm

Dissertations, Theses, and Capstone Projects

In the Atlantic Ocean powerful directional ocean currents can play a significant role in the formation and persistence of marine species. Syngnathidae fishes have a sparse fossil record, high morphological plasticity, and many of these species are difficult to observe in the wild, therefore they frequently lack life history information and the status of regional lineages and species designations are often obscure. In this dissertation I explore the ecology, evolution, and conservation of primarily Atlantic seahorses (Hippocampus) and pipefish (Syngnathus) in four core chapters, using differing genetic datasets ranging from mitochondrial DNA to genome-wide RAD sequences. Most Synganthids have the …

Systematics And Biogeography Of Orthaea Kloztsch (Ericaceae: Vaccinieae), Nelson Salinas

Dissertations, Theses, and Capstone Projects

In the first chapter a study of the distribution patterns of the neotropical Vaccinieae (Ericaceae) is presented. Five areas of endemism were recovered: Central America, northern Chocó, southern Chocó, eastern Ecuador, and Yungas. Divergence times estimations indicate that the Andean clade of Vaccinieae migrated to South America during the Late Oligocene or Early Miocene (28.9-17.84 MA), and most of the subsequent diversification took place during the Tertiary. The Yungas was the first Andean area to be colonized, and several dispersals towards the north expanded their distribution range. Both areas of endemism and dispersal events were influenced by geological processes, such …

Functional Characterization Of The Plant 15-Cis-Zeta-Carotene Isomerase Z-Iso, Jesus Alonso Beltran Zambrano

Dissertations, Theses, and Capstone Projects

Vitamin A deficiency is a widespread health issue in the tropics. To solve this issue, efforts are underway to increase provitamin A carotenoids such as β-carotene in staple crops which can be achieved by breeding, metabolic engineering or a combination of both approaches. However, rational strategies to improve carotenoid content in crops require sufficient knowledge of pathway regulation. Therefore, to better understand how plants synthesize provitamin A and to guide metabolic engineering strategies in crops such as maize, the functional characterization of the new ζ-carotene isomerase (Z-ISO) is of significant importance.

Z-ISO was recently discovered in maize and Arabidopsis (Chen …