Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • Understanding A Pest--Phylogeography And Systematics Of The Plum Curculio (Conotrachelus nenuphar)

    Author:
    Samuel Crane
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Rob DeSalle
    Abstract:

    The plum curculio (Conotrachelus nenuphar Herbst) (Coleoptera: Curculionidae) is an economically and ecologically important pest in North America but is understudied despite having a long history in the scientific literature. Its chemical ecology, life history habits, and distribution are all well characterized. However, there is a dearth of knowledge concerning the population structure and evolutionary history of the species. This study aims to use methods from evolutionary biology to better understand an agricultural pest species and provide tools to aid in its management. Existing taxonomic classifications of North American Conotrachelus species have been tested for the first time. Using a combined multigene approach, we have inferred a species phylogeny. Established species groups are well supported as monophyletic. However, the species groups identified in taxonomic keys are generally not recovered as monophyletic. Broadly sampling across the geographic distribution, we have sample over 1,000 individuals for mitochondrial DNA variation. We characterized population substructure of plum curculio populations from the full breadth of its range and reveal significant geographic and genetic structure. There is a significant north-south split that does not align with the current understanding of the plum curculio phenological strains. There are also highly structured populations corresponding to the Mississippi River and Apalachicola River basin, a pattern thought to be associated with southern refugia along the Gulf Coast. There are likely multiple refugia used over the Last Glacial Maximum. Regions of the world that are most at threat of plum curculio beetle invasion, given the organism's habitat preferences, are identified across all continents and in every region where it is listed as a quarantine species. Molecular tools for diagnosing and managing the plum curculio, locally and internationally, are developed and provided for all life stages.

  • Testing assumptions of coevolution in an egg-rejecting brood parasite host: Uncovering sensory, cognitive, and evolutionary drivers of responses to parasitism in American robins (Turdus migratorius)

    Author:
    Rebecca Croston
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    Mark Hauber
    Abstract:

    Hosts of brood parasitic birds face fitness costs associated with rearing unrelated offspring. In response, the recognition and rejection of parasitic eggs is a common host defense. Brown-headed cowbirds (Molothrus ater) challenge coevolutionary theory, because although they exploit over 200 host species, they lay non-mimetic eggs, and most hosts do not combat cowbird parasitism with egg rejection. American robins (Turdus migratorius) are one of a handful of cowbird hosts known to recognize and remove cowbird eggs from the nest. I addressed the mechanistic and evolutionary drivers of egg rejection in this host species, by disentangling the roles of spectral tuning and visual physiology on the behavioral outcome of egg rejection, by estimating the costs of parasitism which may drive egg rejection behavior, and by addressing the reciprocal effects parasitism on host egg color variation and its role in mediating rejection decisions. I also test assumptions underlying the evolvability of host egg rejection responses in this system. In Chapter 1, I lay out an overview of brood parasitism as a reproductive strategy and brood parasite-host ecology, and highlight evolutionary mechanisms and consequences of coevolution in these systems. In Chapter 2, I test the hypothesis that foreign egg rejection is driven proximately by perceivable differences in ground color between host and parasitic eggs across the entire avian spectral sensitivity range. I show that the rejection of artificially dyed eggs is mediated by input from all four avian single-cone photoreceptors, and that more divergent model `parasitic' eggs are indeed rejected at higher rates. However, the cowbird egg does not conform to this prediction, because both model and real cowbird eggs are rejected in 100% of experimental trials despite their lower overall discriminability from robin eggs. This may indicate a cowbird-egg specific rejection response in robins. In Chapter 3, I test a critical assumption underlying the evolution of cowbird-specific egg rejection responses in robins, by assessing the hypothesis that cowbird parasitism imposes recoverable costs on robin hosts. My results indicate that cowbird chicks fare poorly when reared alongside robin chicks, but parasitism per se still reduces nesting success for robins; thus, rejection of cowbird eggs serves a function to eliminate the cost of parasitism. In Chapter 4, I examine a critical assumption underlying all of host-parasite coevolutionary theory, namely that host defenses can evolve genetically in response to parasitism. I address the hypothesis that egg rejection is repeatable in our study population, as repeatability is prerequisite to the evolution and spread of a behavioral trait, including a predictor of the trait's genetic heritability. As predicted, egg rejection behavior in American robins was found to be highly repeatable for intermediately-rejected model egg colors within the same nesting attempt, irrespective of potentially confounding ecological and temporal factors. Finally, in Chapter 5, I test predictions stemming from alternate hypotheses that egg rejection evolved in response to cowbird (non-mimetic) versus conspecific (mimetic) parasitism, by investigating the degree of color variation within robins' own clutches, and the effect of experimentally manipulating intraclutch color variation. I used both observational and experimental data, and found that egg color varies more between clutches than among egg within a single clutch, yet experimental manipulated intraclutch color variation did not affect rejection rates. These results support the scenario of historical parasitism by non-mimetic parasites. Variation among the findings of similar studies pertaining to hosts of mimetic parasites may be explained by hosts' use of different cognitive mechanisms in the decision to reject foreign eggs, However, for hosts of non-mimetic parasites, investigating egg color variation and its effect on egg rejection is not informative about different cognitive decision-making rules, as predictions under each mechanism are similar - that there will be no effect of a history of parasitism on intraclutch color variation (observational patterns) or rejection rate (experimental data). This body of research presents compelling evidence in support of egg rejection by robins as a specific response to historical cowbird parasitism, and has highlighted important components of the sensory, cognitive, functional and evolutionary processes underlying egg rejection in this paradoxical brood parasite-host system.

  • Systematics and Phylogeny of Arcoid Bivalves (Arcoida: Pteriomorphia: Bivalvia)

    Author:
    Louise Crowley
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Ward Wheeler
    Abstract:

    The Arcoida is a large group of mostly marine bivalves, with a global distribution. Familiar taxa in this group include the arks, bittersweets and dog cockles. Relationships among the higher-level taxa of the Arcoida are not well understood and the classification of this group has been the subject of debate and rearrangement. While many views exist as to the evolution of this group, none of them are based explicitly on a phylogenetic analysis. In this study, the phylogenetic relationship of the Arcoida is inferred from a systematic analysis based on both morphological and molecular data. This is the first analysis in which representatives of all seven nominal families are included. 141 morphological characters from the external shell and internal anatomy were coded for 131 taxa. The phylogenetic signal of both these character types was explored. Few non-homoplastic synapomorphies for the group were recovered; shell tubules are confirmed as the sole non-homoplastic synapomorphy for the order. Shell characters failed to recover the majority of the higher taxonomic ranks that they were initially used to describe. Little coherent signal was received from the analysis of anatomy alone. Four molecular markers, the nuclear 18S rRNA, 28S rRNA, protein coding histone H3 and mitochondrial cytochrome c oxidase I, were also investigated using direct optimization as implemented in POY (Varón et al., 2008). These data were analyzed individually as well as simultaneously with the morphological data. A Sensitivity Analysis (Wheeler, 1995) of the molecular data was also performed--this explores the effects of parameter costs (i.e. indels and transition/transversion ratios) on the phylogenetic results. The results of these phylogenetic analyses do not reflect the current classification of the group. In this study, the majority of the higher taxonomic groups of Newell (1969) were not recovered, including the two superfamilies Arcoidea and Limopsoidea, as well as five of the families; only the monophyly of the Glycymerididae and Noetiidae is supported. A major taxonomic review of the order is necessary. This analysis is the largest and most comprehensive phylogenetic analysis of the Arcoida to date.

  • Molecular genetic studies of sulfur nutrient response in Arabidopsis thaliana

    Author:
    Hanbin Dan
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Zhi-Liang Zheng
    Abstract:

    The aim of this study was to isolate the components that are critical for the S nutrient response in plants. We used Arabidopsis thaliana as a model system. We first developed a S deficiency-responsive promoter:GUS reporter system. We confirmed that At2g44460 encoding a putative thioglucosidase exhibits the strongest induction by S deficiency. Interestingly, At2g44460 induction by S deficiency was suppressed by the application of auxin, a plant hormone. Together with other physiological and genetic evidence, we showed that auxin plays a negative regulatory role in S deficiency response. Furthermore, we found that S deficiency-induced expression of At2g44460 and a sulfate transporter gene (SULTR4;2) is dependent on the availability of C and N, which exhibit a synergistic interaction. Therefore, we designed a genetic screen by using the At2g44460 promoter:GUS reporter line (designated GHF1) with an aim of isolating the mutants that alter the expression of At2g44460 in response to C,N and S status. Screen of the mutants resulted in the isolation of two allelic mutations on the SEL1 gene, which encodes a high-affinity transporter called SULTR1;2. SULTR1;2 is mainly responsible for transporting sulfate from the soil into the root. The two alleles, designated sel1-15 and sel1-16, have distinct missense mutations on the putative transmembrane domains, but they did not seem to cause mislocalization of the protein. As expected, these two mutations, like a SULTR1;2 null allele (sel1-10), abolish the sulfate uptake in both yeast and plant systems. They also reduced the accumulation of internal sulfate. However, a dose response study indicates that expression of the S deficiency-upregulated genes, At2g44460, SULTR4;2, LSU1 and SDI1, is higher in the mutants than that in WT under either the high sulfate treatment or under different sulfate treatments that result in similar levels of internal sulfate. Furthermore, these mutants reduced the sensitivity to external application of the high concentration of sulfate metabolites, suflite, Cys and GSH. Taken together, these results indicate that besides the sulfate transport function, SULTR1;2 likely acts as a sensor for S nutrient, adding this transporter to the growing list of nutrient transceptors.

  • Q'eqchi' Maya Reproductive Ethnomedicine, Estrogenic Plant Use, and Women's Healing Traditions in Belize

    Author:
    Jillian De Gezelle
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Michael Balick
    Abstract:

    The Q'eqchi' Maya of Belize have an extensive ethnopharmacopoeia of medicinal plants used traditionally for reproductive health and fertility. Ethnobotanical research was carried out in the Q'eqchi' communities of the Toledo District of Southern Belize from 2007-2011 on medicinal plant species used for reproductive health. Data was gathered primarily through semi-structured interviews and plant collecting trips with 6 traditional healers, 3 midwives, and 12 female herbalists. The Belizean Q'eqchi' are utilizing more than 60 plant species for reproductive health treatments, with the most species from the family Piperaceae. Ten species were selected for investigation of their estrogenic activity using a reporter gene assay: Clidemia crenulata Gleason, Drymonia serrulata Jacq. (Mart.), Gouania lupuloides (L.) Urb., Miconia oinochrophylla Donn. Sm., Mimosa pudica L., Piper jacquemontianum Kunth, Piper peltatum L., Psychotria acuminata Benth., Psychotria poeppigiana Müll. Arg., and Tococa guianensis Aubl. These plants are used to treat female infertility, male infertility, menopausal symptoms, heavy menstruation, uterine fibroids, k'uub'sa' (a Q'eqchi' womb disorder), for miscarriage prevention, for use as female contraception, and for male contraception. Methanol extracts of the leaves of all species were assayed, as well as the stems of G. lupuloides, roots of M. pudica, and the roots of P. peltatum. All the extracts displayed estrogenic activity, except for M. pudica roots and P. jacquemontianum leaves, which were both cytotoxic to the MCF-7 breast cancer cell line. Nine of the species assayed were estrogenic, four of the species were also antiestrogenic, and two of the extracts were cytotoxic to the MCF-7 cell line. Women's healing traditions are being lost in the Q'eqchi' communities of Belize at an accelerated rate, due to a combination of factors including: migration from Guatemala disrupting traditional familial lines of knowledge transmission; perceived disapproval by local biomedical authorities; women's limited mobility due to domestic obligations; and lack of confidence stemming from the devaluation of women's traditional knowledge. Medicinal plant knowledge is highly gendered with women and men commonly using different species in reproductive health treatments. Revitalizing women's healing practices is vital for maintaining the traditional knowledge needed to provide comprehensive healthcare for Belize's most remote indigenous communities.

  • COMPARATIVE PHYLOGEOGRAPHY, PHYLOGENETICS, AND POPULATION GENOMICS OF EAST AFRICAN MONTANE SMALL MAMMALS

    Author:
    Terrence Demos
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    Michael Hickerson
    Abstract:

    The Eastern Afromontane region of Africa is characterized by striking levels of endemism and species richness which rank it as a global biodiversity hotspot for diverse plants and animals including mammals, but has been poorly sampled and little studied to date. Using mtDNA and multi-locus nDNA sequence data, genome-wide RAD-Seq SNP data, and morphological data, I identify major cryptic biogeographic patterns within and between 11 co-distributed small mammal species/species groups across the Eastern Afromontane region. I focus on two endemic montane small mammal species complexes, Hylomyscus mice and Sylvisorex shrews, co-distributed across the Albertine Rift (AR) and Kenya Highlands (KH) of the Eastern Afromontane Biodiversity Hotspot. I characterize patterns of phylogeographic structure, demographic history, phylogenetic relationships and undescribed biodiversity across these taxa. Putative independently evolving lineages are inferred using a combination of distribution data, coalescent species delimitation and historical demographic inference. Hypotheses put forward to account for the high diversity of the region include both retention of older palaeo-endemic lineages across major regions in climatically stable refugia, as well as the accumulation of lineages associated with more recent differentiation between allopatric populations separated by unsuitable habitat at the LGM. Populations have persisted since the Pliocene to mid-Pleistocene across a climatic gradient from the AR in the west to the KH in the east for both focal taxa. Deeply divergent and sympatric cryptic lineages, previously unidentified, are strongly supported in both mice and shrews, highlighting the broad temporal scale at which cyclical climatic changes over the last 5 Ma may have contributed to high species diversity and endemism in the Eastern Afromontane Hotspot. Complete genome-wide SNP matrices for Hylomyscus and Sylvisorex are used in population genetic analyses that support lineages not uncovered by the 3-6 locus dataset. Graphs of population splits and admixture support substantial gene flow from AR into KH shrew populations subsequent to isolation that occurred 2.5-3.5 million years earlier, possibly by intermittent colonization. A new species, Hylomyscus kerbispeterhansi, is described from Kenya using combined morphological and multi-locus data sets.

  • Glutamate Receptor Signaling is a Mediator of Neurite Outgrowth Inhibition

    Author:
    Sarit Derey
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Marie Filbin
    Abstract:

    Unlike the peripheral nervous system (PNS) or embryonic neurons, the adult mammalian central nervous system (CNS) does not spontaneously regenerate after injury. This is due, in part, to the presence of myelin-associated inhibitors, such as myelin-associated glycoprotein (MAG). Our lab has shown that elevation of intracellular cAMP blocks these inhibitors in vitro and in vivo in a transcription-dependent manner. Subsequent microarray analysis revealed that elevation of cAMP results in upregulation of Arginase I (Arg1), a key enzyme in the synthesis of polyamines. Our lab has demonstrated that administration of polyamines is sufficient to block MAG and myelin-induced inhibition of axonal outgrowth in vitro as well as enhance CNS axon regeneration in vivo. Others have shown that binding of polyamines to ionotropic glutamate receptors (iGluRs), which include N-methyl-D-aspartate receptors (NMDAR), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), and kainate receptors (KAR), blocks their activity. In addition, it is well established that iGluR activity is disrupted following CNS injury. Thus, since polyamines overcome MAG/myelin-mediated inhibition and given that polyamines block iGluRs activity, we set out to examine the role iGluR-mediated signaling plays in the MAG and myelin inhibitory pathways. We found that blocking NMDAR or AMPA/KA receptor activity with pharmacological antagonists was sufficient to block MAG-induced inhibition of neurite outgrowth in dorsal root ganglia (DRG) and hippocampal neurons (HNs). Likewise, exposure to iGluR agonists increased MAG-mediated inhibition of neurite outgrowth. To determine whether prior exposure of iGluR inhibitors or priming is sufficient to overcome MAG inhibition as in the case of polyamines, HNs were treated with iGluR antagonists 18 hours before exposing neurons to MAG. We found that priming with iGluR antagonists was not sufficient to overcome MAG-mediated inhibition, suggesting that GluR antagonists exert their effect by intercepting MAG inhibition signals, while not changing the ability of neurons to respond to MAG. Because polyamines require priming whereas iGluR antagonists have no effect when used to prime neurons, we therefore conclude that in our model system, polyamines do not overcome inhibition by blocking iGluR activity. It is well established that upon activation, NMDARs produce influx of Ca2+ inside the cell, which activates Ca2+-dependent kinases such as extracellular signal-regulated kinase (ERK) and conventional protein kinase C (PKC), both of which are important for synaptic plasticity, long term potentiation (LTP), and long term depression (LTD). Importantly, conventional PKC and epidermal growth factor receptor (EGFR)-regulated ERKs are also known to be activated in response to myelin inhibitors in a Ca2+-dependent manner. Blocking PKCs or EGFRs is sufficient to overcome inhibition by myelin inhibitors in vitro and promote axonal regeneration in vivo. To establish which downstream target activation is affected in response to iGluR activity block as well as myelin, PKC and ERK signaling pathways were examined. We found that myelin induces robust ERK activation, and importantly, inhibiting iGluR activity was sufficient to block ERK activation. Next, to determine whether myelin-induced ERK activation is inhibitory for neurite outgrowth, HNs were treated with the ERK inhibitor U0126 and then subjected neurite outgrowth assay in the presence of MAG. We found that blocking ERK was sufficient to overcome MAG-mediated inhibition in a dose dependent manner. Our findings demonstrate that exposure to myelin induces ERK activation and that ERK activation is regulated by iGluR activity. Since ERK is one of the main downstream targets activated by NMDAR-induced Ca2+ influx, our findings support the idea that exposure to myelin results in iGluR activation. In synapses, repeated activation of NMDAR leads to long-term potentiation (LTP) through mechanisms involving the activation of PKC and ERK as well as rapid forward trafficking of NMDARs to the membrane. This is consistent with reports that PKC induces phosphorylation in the C-terminal of the NMDA NR1 subunit, leading to increased surface insertion of NMDAR channels. To determine whether myelin-associated inhibitors affect NMDAR trafficking, cortical neurons were treated with myelin and then the amounts of surface NMDARs was assessed. We found that myelin induced a rapid increase in surface NMDAR number. In addition, myelin treatment induced phosphorylation of ser890 and ser896 C-terminal NMDA NR1 subunits, which have been shown to promote forward NMDAR trafficking to the cell surface. Thus, our findings suggest that myelin-induced PKC activation promotes surface incorporation of NMDARs, which can potentially enhance NMDAR-mediated currents. Taken together, our results implicate iGluR activity as well as ERK signaling as new mediators of MAG/myelin-induced inhibition, offering new insights into the molecular mechanism of myelin-induced block of neurite outgrowth.

  • Polymerase alpha components associate with telomeres to mediate overhang processing

    Author:
    Raffaella Diotti
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    Diego Loayza
    Abstract:

    Telomeres consist of TTAGGG repeats, which end with a 3' G-overhang and are bound by a six-protein complex, known as Shelterin. In humans, telomeres shorten at each cell division, unless telomerase is expressed and able to add telomeric repeats to the 3' G-overhang. However, for effective telomere maintenance, the DNA strand complementary to that made by telomerase must be synthesized. In this study, I focused on the Polα/primase complex, in particular the subunits p68 (POLA2, the regulatory subunit) and p180 (Polα, the catalytic subunit), and their potential roles at telomeres. I was able to detect p180, p68 and OBFC1, a subunit in the CST complex, at telomeres in S phase using chromatin immunoprecipitations. I could also show that OBFC1, Shelterin and Polα/primase interact, revealing contacts occurring at telomeres. Finally, depletion of p68 by shRNA and p68 and p180 by siRNA, led to increased overhang amounts at telomeres. I propose a model in which Polα-primase is important for proper telomeric overhang processing, perhaps through fill-in synthesis. These results shed light on important events necessary for efficient telomere maintenance and protection.

  • Functional Diversity of Fibroblast Growth Factor Homologous Factor Family of Proteins

    Author:
    Katarzyna Dover
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Mitchell Goldfarb
    Abstract:

    Abstract “Functional Diversity of Fibroblast Growth Factor Homologous Factor Family of Proteins” by Katarzyna Dover Thesis Advisor: Dr. Mitchell Goldfarb FHFs resemble other fibroblast growth factors on a basis of amino acid composition and crystal structure but evolved to carry on distinct, FGF unrelated functions. To date, FHFs have been implicated most clearly in modulation of voltage gated sodium channels (VGSCs). FHFs are the classical example of an increase in gene diversity through the alternative promoter usage and splicing. Hence, the multiplicity of isoforms makes this family of proteins an interesting yet, challenging research topic. Different isoforms of FHFs have distinct sub-cellular localizations and differently modulate voltage gated sodium channels. By influencing critical parameters of channel physiology, including voltage dependence of channel steady-state inactivation, recovery from inactivation and current density, the FHF family of proteins has emerged as important regulators of cellular excitability. The role of different FHF isoforms in modulation of VGSCs and their influence on cellular excitability is the main topic of this thesis. Performed experiments aimed to: (i) establish a channel-binding surface, common to all FHFs, (ii) categorize major FHF isoforms into functional groups based on the ability to modulate sodium channel Nav1.6, (iii) elucidate the mechanism involved in A-type FHF induced long-term, use-dependent channel inactivation, and (iv) determine potential differential localization of A-type FHFs in the brain and in subcellular compartments of cerebellar, hippocampal and sensory neurons.

  • Colletotrichum gloeosporioides s.l. in North America: Sex, Host, and Habitat-mediated Diversity in a Plant-associated Ascomycete

    Author:
    Vinson Doyle
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Amy Litt
    Abstract:

    Determining the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. Through intensive regional sampling that encompasses multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North American strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework and characterized some of the factors that influence species diversity. We have developed polymorphic microsatellite markers for C. fructivorum, a species determined to be responsible for cranberry fruit-rot in agricultural areas throughout North America, in order to understand the biotic and abiotic factors that shape populations within the species complex. These markers amplify across several species within the C. gloeosporioides species complex and some are variable within two species, C. rhexiae and C. kahawae, that are closely related to C. fructivorum. Broad geographical and fine-scale hierarchical sampling of C. fructivorum and C. rhexiae coupled with multilocus genotyping has allowed us to gain insight into the forces that shape populations of these species. Human-mediated dispersal is an important factor dissipating the population structure of C. fructivorum throughout its range in commercial cranberry bogs. In contrast, limited evidence suggests C. rhexiae is geographically structured within a more restricted range, implying distinct patterns of diversity between Colletotrichum species associated with wild versus agricultural hosts. We also investigate the reproductive mode of C. fructivorum using estimates of haploid disequilibrium and genotypic diversity, inferring a mixed (sexual and asexual) mode of reproduction in field populations. We discuss the importance of sexual and asexual reproduction on population dynamics and speciation within the C. gloeosporioides species complex.