Alumni Dissertations

 

Alumni Dissertations

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  • Evolution of Song Culture in the Zebra Finch

    Author:
    Olga Feher
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Ofer Tchernichovski
    Abstract:

    Cumulative cultural evolution is when behavior in subsequent generations of learners builds on the accumulated information of previous generations to such an extent that no individual learner can produce the behavior on its own. Many examples exist in humans, but in nonhuman animals there are only a handful of suspected cases. Here, we provide the first demonstration of cumulative cultural evolution in the laboratory in nonhuman animals. We raised zebra finches in complete acoustic and social isolation to create "uncultured" animals. Isolate zebra finches sing unstructured songs that are different from wild-type songs in many aspects such as spectral details of syllables and syntactic organization. We developed an automated procedure to quantify the differences between isolate and wild-type song at different timescales of song structure: spectral features, duration of sounds, and song rhythm. We then used the isolate birds to teach their songs to juveniles who became the tutors for the next generations of learners and so on recursively. We followed the evolution of isolate song over multiple generations. We found that isolate song was gradually transforming into wild-type song over 3-4 learning generations. In addition to this experiment where we trained young birds in individual tutor-pupil pairs, we established a semi-natural colony with an isolate founder and tracked song changes over multiple generations of learners. In the colony, the song also progressed towards wild-type song in a few generations, but some of the details of the changes differed between the two conditions. The rapid evolution indicates that wild-type song culture is encoded in every bird, but it takes multiple generations to surface. The young birds used imitation biases to change isolate song features into wild-type features.

  • C. elegans ADAMTS ADT-2 regulates body size and cuticle collagen organization

    Author:
    Thilini Fernando
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Cathy Savage-Dunn
    Abstract:

    The regulation of body size is a fundamental feature of animals critical to their survival and fitness, yet its underlying mechanisms remain poorly understood. In C. elegans, the DBL-1 signaling pathway plays a major role in growth control. The mechanisms by which other pathways regulate body size function, however, are less well understood. To identify additional genes involved in body size regulation, a genetic screen for small mutants was previously performed. One of the genes identified in that screen was sma 21. I now demonstrate that sma 21 encodes ADT-2, a member of the ADAMTS (a disintegrin and metalloprotease with thrombospondin motifs) family of secreted metalloproteases. ADAMTS proteins are believed to remodel the extracellular matrix (ECM) and may modulate the activity of extracellular signals. Genetic interactions suggest that ADT-2 acts in parallel with known size regulatory pathways. I further demonstrate that ADT-2 activity is required for normal cuticle collagen fibril organization and adt-2 regulatory sequences drive expression in glial-like cells. ADT-2::GFP fusion protein is localized in the alae and the annuli of the cuticle. We therefore show that ADT-2 is secreted into the cuticle where it may act to proteolytically process secreted collagen or other ECM molecules required for normal cuticle structure and body size.

  • The effects of chronic habitat degradation on the physiology and metal accumulation of eastern oysters (Crassostrea virginica) in the Hudson Raritan Estuary

    Author:
    Allison Fitzgerald
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    William Wallace
    Abstract:

    The Hudson Raritan Estuary (HRE) was once home an abundant population of the eastern oyster, Crassostrea virginica. Years of habitat degradation, via removal of habitat and shell substrate, overfishing of the population, and inputs of organic and inorganic contaminants, all led to the decline of this previous keystone species. The HRE today is a highly eutrophic environment, with increased sediment inputs, periods of low dissolved oxygen, algal blooms, and hotspots of contaminants throughout. The current study was designed to understand how a chronically degraded habitat, as is present in the HRE now, affects both juvenile and adult oyster physiology. There are three parts to this study: in the first, a large scale field transplant study was deployed to determine how juvenile oyster health and subcellular physiology are altered over a continuum of sites across the HRE, and if subcellular metal accumulation related to alterations in physiology. Using eight sites across the HRE, it was apparent that there are many site-specific factors that affect oyster physiology, and the synergistic effects of these abiotic and biotic factors together influence oyster physiology the most. There was no one factor that could be isolated as a key parameter to determine future oyster restoration. The second part used a field transplant study to examine the role of a degraded habitat on adult oysters and reproduction. Using Vitellogenin protein and energy expenditures to estimate oyster reproduction, it was seen that adult oysters respond much slower than juveniles and no differences were seen between highly degraded habitats and less degraded habitats. Thirdly, both juveniles and adults were observed to accumulate non-essential metals (Cd and Hg) in the field. In order to determine if metal accumulation is the sole cause of physiological alterations, a laboratory exposure was designed to determine if changes in subcellular physiology could be correlated specifically to subcellular accumulation of Cd or Hg, when no other abiotic factors are able to influence oyster health. It was observed that Cd accumulation lead to physiological changes, but Hg accumulation did not. Using this information about the site-specific nature of oyster physiology and how metal accumulation can alter physiology will allow researchers to choose future restoration sites and set up projects that will allow for maximum growth and survival.

  • EVOLUTION, PHYLOGEOGRAPHY AND SPECIES BOUNDARIES OF THE RINGNECK SNAKE GENUS DIADOPHIS

    Author:
    Frank Fontanella
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Mark Siddall
    Abstract:

    EVOLUTION, PHYLOGEOGRAPHY AND SPECIES BOUNDARIES OF THE RINGNECK SNAKE GENUS DIADOPHIS ADVISER: Dr. Mark E. Siddall The monotypic snake genus Diadophis Baird and Girard, 1853 is one of the most widely distributed and morphologically variable snakes throughout North America. This snake (Diadophis punctatus) exploits a variety of habitats and ecological niches ranging from the mixed hardwood forests of southern Canada to the desert of the Southwestern US and Central Mexico (excluding the northern Great Plains states. Ringneck snakes have traditionally been divided into 13 subspecies based on a combination of morphology and geography. This study has provided the first range-wide molecular study and provides a framework for the origin, evolution and biodiversity in the genus Diadophis. Analysis of mtDNA sequence data inferred 16 mtDNA lineages that replace each other geographically across the United States and into central Mexico. In contrast to previous hypothesis, ancestral area reconstructions inferred an origin for D. punctatus in the southeastern United States during the Miocene, followed by a southeast to northeast then westward directionality of historical migration. Demographic analyses indicate that independent lineages currently occupying previously glaciated or unsuitable areas in eastern, central and western U.S. underwent post-glacial population expansion likely from southern refugia during the late Pleistocene/early Holocene. Conversely, southern lineages display patterns consistent with long-term population stability. For the purposes of species delineation, ecological niche modeling does not show isolation due to unsuitable habitat. Ten novel microsatellite loci developed for this study suggest that most species boundaries are maintained through a balance of selection and dispersal in hybrid zones. Based on the geographic distribution of the mtDNA lineages and the microsatellite frequency data, we hypothesize that there are eight species within the genus Diadophis throughout the Eastern United States. This body of work provides a rich framework for further study including, examining species boundaries in the western lineages, determining population structure within species, and detailed examination of hybrid zones.

  • Phylogenetics, biogeography and co-adaptation between a Batesian model (Micrurus fulvius) and mimic (Lampropeltis triangulum)

    Author:
    Michael Friedman
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Rob DeSalle
    Abstract:

    The coral snake, Micrurus fulvius (Elapidae), and the scarlet king snake, Lampropeltis triangulum (Colubridae), members of a Batesian mimicry complex in the southeastern and southern United States were subjects of a study of model-mimic co-evolution. Inferring co-evolution required discovery of distinct terminals within each group, for posterior phylogenetic inference and analysis of co-variation of color patterns among sympatric populations of each species. In addition, haplotype and population differentiation were assessed. Also, hypotheses regarding selection on color patterns were tested. The latter included model-mimic tracking, environmental effects and frequency dependence of mimetic color pattern variation. Population Aggregation Analysis failed to diagnose terminals for either group. Haplotype and population genetic analyses showed both groups to be largely panmictic, with some north/south differentiation. Morphometric analyses of means and variations in proportions of color pattern components failed to reveal geographic tracking by mimics of models, but manifested possible independent geographic or environmental effects on each of the species. Frequency-dependent selection was falsified for color pattern variation in mimics.

  • Islet-brain-2: a novel postsynaptic density protein linked to an autism spectrum disorder

    Author:
    Joanna Giza
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Mitchell Goldfarb
    Abstract:

    Islet-brain-2 (IB2) is a neuronal protein, whose functions are not well understood. Based upon its sequence homology to JNK-interacting protein 1 (JIP1) and biochemical studies, IB2 has been described as a putative scaffold for mitogen activated protein kinase (MAPK) signaling. IB2 has been documented to interact with a wide array of functionally unrelated proteins, which has complicated efforts to confirm its biochemical role in vivo. In order to investigate the IB2 function in the nervous system, we have generated Ib2 null mice. The mutants are viable and their expression of genes neighboring Ib2 is unaffected. Ib2 knockout mice display developmental delay in grip strength until 5 weeks (P35) of age. Their behavioral analysis following disappearance of this defect shows significant deficits in their motor learning abilities. In addition, mutant mice exhibit marked reduction in social interactions, delayed fear induced learning and unresponsiveness to the environment in various behavioral tasks. These complex atypical behaviors are reminiscent of autism spectrum disorders (ASDs). Interestingly, the human Ib2 gene resides within the deleted chr22qter region in Phelan-McDermid syndrome and patients with this disorder manifest similar deficits as observed in our Ib2 null mice, suggesting that Ib2 loss-of-function is a promising candidate model for this disorder. Recent developments in the ASDs field implicate as a major culprit defective synaptic function. Using brain fractionation and co-immunoprecipitation methods, we show that IB2 is an integral component of the postsynaptic density (PSD). Immunofluorescence shows IB2 concentrated within dendritic spine heads. Ib2 mutation did not alter expression levels of many other common PSD components such as PSD95 and AMPA-type and NMDA-type receptors subunits. Signaling analyses conducted in Ib2 null cultured cortical neurons failed to reveal deficits in NMDA-evoked signaling through known IB2-interacting partners TIAM1 and p38MAPK, suggesting that IB2 modulates synaptic and behavioral functions through as yet unknown molecular mechanisms.

  • MAG and myelin block the ability of BDNF to overcome inhibition of axonal regeneration by inhibiting BDNF's activation of Rap1

    Author:
    Vasiliki Gkioka
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Marie Filbin
    Abstract:

    It is well established that axons of the adult mammalian CNS do not regenerate if injured by trauma, or if afflicted by various neurodegenerative conditions. It is also well established that myelin, the insulating and protective membranous sheath around neurons, contains several proteins that act as inhibitors of neurite outgrowth, such as MAG, and damaged myelin is one of the factors limiting CNS regeneration after injury. Because of their well established role in neuronal development, survival, and function, neurotrophins have been candidates for therapeutic intervention in the nervous system for many years, and have already been used in clinical trials for various neurological conditions. We have previously shown that neurotrophins elevate cAMP. If the cAMP signaling cascade is initiated in neurons exposed to MAG and myelin, with the non-hydrolyzable analogue dibutyryl-cAMP, inhibition of neurite outgrowth by both is blocked in vitro. Importantly, we have shown that if cAMP is elevated in damaged neurons, nerve regeneration is promoted in vivo. We have also observed that neurotrophin-induced cAMP elevation is blocked in the presence of MAG, and neurotrophins are effective in overcoming MAG inhibition only by overnight pre-exposure of neurons to them, a procedure we call "priming with neurotrophins". Therefore, understanding the mechanism of MAG and myelin's block of neurotrophin signaling could result in the design of therapeutics that target only specific molecules in the neurotrophin cascade, in order to potentiate only specific and desirable effects of neurotrophins, for specific types of injury or disease. We have found that MAG and myelin block the BDNF activation of Rap1, one of the Ras-superfamily members activated in the neurotrophin cascade, which is also part of the cAMP signaling network, due to cAMP-activation of one of its upstream activators, EPAC. We have also shown that MAG and myelin treatment of neurons results in upregulation of the protein levels of the Rap1 inactivator Rap1GAP, which provides a mechanism for the block of Rap1 activation by BDNF. Additionally we have shown that priming of neurons with the EPAC-specific cAMP analogue 8-CPT-2Me-cAMP, like priming with neurotrophins, is sufficient to overcome inhibition by MAG. Moreover, infection of neurons with adenoviruses carrying wild type Rap1, or the RapGAP insensitive mutant Rap1F64A, improved growth on MAG and myelin. Infection of neurons with adenovirus carrying the Rap1 inactivator Rap1GAPI blocked the ability of neurons to extend neurites, demonstrating an essential role of the Rap1 family in regulating neurite outgrowth. Besides its implications for therapeutic intervention after CNS trauma, the modulation of the neurotrophin cascade by MAG demonstrated here might be a new manifestation of the role of MAG and myelin in restricting plasticity in the intact CNS.

  • Systematics of the North American Scorpion Subfamily Syntropinae ( Scorpiones: Vaejovidae)

    Author:
    Edmundo Gonzalez
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Lorenzo Prendini
    Abstract:

    The first phylogenetic analysis and a taxonomic revision of the North American vaejovid scorpion subfamily Syntropinae Kraepelin, 1905 are presented. The phylogeny is based on a simultaneous analysis of molecules (5 loci) and morphological characters (continuous and discrete). The current classification of the subfamily (Soleglad and Fet, 2008) was tested for monophyly and the relative positions of insertae sedis taxa putatively related to the subfamily were investigated. Nodal stability and nodal support for the resultant topologies were high; although the molecules and morphology had dissimilar phylogenetic signals simultaneous analyses enhanced the overall signal and thus generated the hypothesis with the most explanatory power. Syntropinae and Stahnkeini Soleglad and Fet, 2008 were recovered as monophyletic. The Syntropinae comprised six monophyletic groups that contradicted the current classification. The following taxonomic emendations are proposed. The tribe Paravaejovini Soleglad and Fet, 2008 and the subtribe Thorellina Soleglad and Fet, 2008 are synonymized with Syntropinae; the Syntropinae is redefined with eleven genera. Six new genera are described, Balsateres n. gen., Chihuahuanus, n. gen., Konetontli, n. gen., Maaykuyak, n. gen., Mesomexovis, n. gen., and Vizcaino, n. gen. Hoffmannius, syn. n. is synonymized with Paravaejovis and 15 species are transferred to other genera. Five subspecies are elevated to species, two restored from synonymy and 26 new species are described. Possible scenarios of the evolution and distributional pattern of the genera and species are presented, from a historical and ecological perspective.

  • Functional Genomics of Cell Wall Biogenesis in Fungi

    Author:
    Edimarlyn Gonzalez
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Peter Lipke
    Abstract:

    In pathogenic fungi, glycosylphosphatidyl inositol cell wall proteins (GPI-CWPs) mediate adhesion of the fungus to a host during infection -a step that is necessary for the fungus to be able to initiate and establish infection. Genes involved in the biosynthetic pathway that incorporate GPI-CWPs to the wall thus represent excellent targets for antifungal drug design. A mechanistically-based genomic screen was developed and applied to search for genes involved in fungal cell wall biogenesis. Specifically, the screen identifies genes required for the cross-linking of glycoproteins (GPI-CWPs) to cell wall polysaccharides via GPI anchors. GPI-CWPs are the most abundant class of proteins at the wall and play both structural and biosynthetic functions. The rationale for the screening assay was that cells unable to properly cross-link GPI-CWPs to the wall would either retain a GPI-CWP reporter protein within the cell (hypo-excretors) or excrete the reporter protein into the growth medium (hyper-excretors), relative to wild type cells. This idea was validated in cell wall mutants known to hyper-excrete GPI-CWPs. To screen for the hypo- and hyper-excretion phenotypes, a GPI-CWP-marker protein was made by fusing the green fluorescent protein (GFP) to the carboxyl end of the GPI-CWP α-agglutinin. The marker protein was expressed in 178 gene deletants missing genes previously implicated in cell wall biogenesis and in corresponding wild type parental strains. Strains expressing the reporter protein were examined for deficiencies in anchoring the marker protein to the wall. The screen used conditions that facilitated sample processing at large-scale and enhanced marker protein yields while minimizing noise in marker protein expression. These conditions required expression of the reporter protein from the constitutive S. cerevisiae GPD1 promoter at lower temperature than the standard 30 0C in the presence of 1 M sorbitol, and growth of the cell cultures to similar cell concentrations in medium buffered to pH 6.5. Sample analysis at large scale was possible by growing the cells as 3 ml cultures in glass test tubes from which OD measurements were taken directly. Microliter volumes of cell-free supernatants were evaluated for GFP levels using a 96-well plate reader fluorimeter. Interesting mutants were subjected to secondary screens using anti-GFP antibodies and by collecting complete fluorescence spectra. The strains were also analyzed for cell surface fluorescence and levels of cytosolic and total protein in the culture medium. Deletions in MCD4, GPI13, TDH3 and GDA1 caused hyper-excretion of the reporter protein. MCD4 and GPI13 are essential genes that play a role in GPI-anchor biosynthesis, GDA1 is involved in GPI-CWP O-glycosylation and TDH3 is a glycolytic enzyme that resides at the cell wall and has been implicated in mediating adhesion of fungal cells to host surfaces. The genomic screen was performed without the use of pepstatin A, which was found to inhibit GFP degradation by extracellular protease activity and thus to enhance the sensitivity of the screening assay without affecting cell growth and viability. Identified mutants thus hyper-excrete large enough amounts of the GPI-CWP reporter protein to allow detection of the hyper-excretion phenotype even in the presence of GFP proteolysis. Deletion of the transglycosidases Dcwp1 and Dfg5p, suspected of playing a direct role in cross-linking GPI-CWPs to the cell wall, hyper-excreted the reporter protein when grown in the presence of pepstatin A. Gene deletants subjected to secondary screens exhibited 1.5-2.0 fold less fluorescence at the wall than wild type cells except for MCD4/mcd4 and GPI13/gpi13 cells which hyper-express the marker protein at the wall 2-4-fold relative to wild type cells. This increase may be in compensation for the high failure rate of adding the GPI-anchor to GPI-CWPs precursors. All strains examined showed less than wild type levels of the cytosolic marker, 3-phosphoglycerate kinase (PGK) and wild type levels of total protein in cell-free supernatants.

  • HOW IMPORTANT IS LAND-BASED FORAGING TO POLAR BEARS (URSUS MARITIMUS) DURING THE ICE-FREE SEASON IN WESTERN HUDSON BAY? AN EXAMINATION OF DIETARY SHIFTS, COMPOSITIONAL PATTERNS, BEHAVIORAL OBSERVATIONS AND ENERGETIC CONTRIBUTIONS.

    Author:
    Linda Gormezano
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    Robert Rockwell
    Abstract:

    Trophic mismatches between predators and their prey are increasing as climate change causes decoupling of phenological relationships. Predators linked to the life histories of a particular prey will have a more difficult time persisting through environmental change unless they can alter their behavior to maintain the historical match or possess the ability to pursue alternate prey. Arctic predators typically possess flexible foraging strategies to survive in the labile environment, however, quantifying the limits of those strategies can be difficult when life history information is incomplete. In such cases, piecing together different aspects of a predator's foraging behavior, particularly when environmental effects are thought to induce the most nutritional stress, can serve as a basis to understand the species' resiliency in response to climate changes. Climate change is impacting the Hudson Bay region faster than any other portion of Arctic North America. As a consequence, polar bears (Ursus maritimus) in western Hudson Bay, near the southern extent of their range, are already experiencing a phenological mismatch with their primary prey, ringed seals (Phoca hispida). These polar bears have relied on the energy stores amassed from hunting seal pups in spring to sustain them through the ice-free season on land for 4 to 5 months. As climate change causes the ice in Hudson Bay to melt earlier in spring, polar bears are projected to have less time to hunt seal pups on the sea ice, leaving them with smaller energy reserves to sustain them for longer periods on land. As a result, body condition is expected to deteriorate, leading to eventual declines in reproduction and survival, unless alternative energy sources are utilized. Polar bears currently hunt and consume a variety of foods during the ice-free season. Few believe, however, that such foraging will compensate for projected energy deficits from lost seal hunting opportunities. This skepticism stems from the perceptions that polar bears are specially adapted to hunting seals on the ice, the behavior has always occurred, but only a few polar bears partake in it, breath-based carbon-isotope analyses suggest that energy expended on land is solely of marine (i.e., seal) origin, pursuing animals on land would be too energetically expensive for polar bears to experience any net gain and there is not enough energy in land-based food to compensate all polar bears in western Hudson Bay for the energy available from seals on the ice. Many of these arguments are premised on the idea that past (and even present) foraging behaviors are representative of how polar bears will respond to future climate-related changes. Alternatively, the past behaviors may have represented optimal foraging strategies when seals were relatively abundant and easy to catch. Rather than tie the polar bears' fate directly to deteriorating ice conditions and thus availability of a single prey, I consider a more mechanistic approach to evaluating polar bears' reaction to climate changes. In light of the shared genetic legacy with grizzly bears, I analyze different aspects of polar bears' current foraging behavior, as well as known physiological and energetic constraints, to consider an alternative future scenario by which polar bears might persist consuming land-based food during the ice-free season. I explore different aspects of land-based foraging and address aforementioned concerns regarding the potential value of terrestrial foods in a series of interrelated chapters. In the first chapter, I develop a comprehensive inventory of foods polar bears currently consume on land and compare them to those consumed approximately 40 years earlier, prior to the onset of climate changes, using morphological scat analysis. Changes in the polar bear diet between time periods are compared to changes in availability of specific prey items in the region (Chapter 1) as well as where and when they currently occur most abundantly in the landscape (Chapter 2). Based on compositional patterns, I explore the extent of diet mixing and its implications for weight gain (or rate of weight loss, Chapter 2). In addition to long-term changes in abundance that have made Lesser Snow Geese (Chen caerulescens caerulescens) more available since the 1960s, temporal shifts in their incubation period and earlier ice-breakup is creating a new trophic match between arriving polar bears and eggs. The potential energy available from this increasingly accessible resource and its implications for energy compensation are discussed in Chapter 3. In Chapter 4, I provide total energy values for populations of novel animal foods (snow geese, eggs, caribou (Rangifer tarandus) and vegetation (berries, Lyme grass seed heads (Leymus arenarius) that polar bears consume on land and determine what amounts of each, alone or in combination, would prevent adult males from starving to death as the ice-free season expands to a 180 days as predicted by Molnár et al. (2010). In Chapter 5, I reexamine available data on the energetic costs of locomotion at different speeds, develop a new predictive model and challenge past assertions by Lunn and Stirling (1985) that energetic inefficiencies would prevent a polar bear from profiting after a sustained chase. In Chapter 6, I present unpublished observations of polar bears foraging from land and in open water from the Hudson Bay Project archives and my personal observations. I describe different evolutionary pathways for the observed behavior in light of their recent divergence from grizzly bears and the implications of each for future polar bear persistence.