Alumni Dissertations

 

Alumni Dissertations

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  • Biodiversity and Ethnography of Tea Management Systems in Yunnan, China

    Author:
    Selena Ahmed
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Charles Peters
    Abstract:

    This study investigates biodiversity and cultural practices associated with tea (Camellia sinensis (L.) O. Kuntze; Theaceae) management systems in Yunnan Province of southwestern China. Surveys were conducted in smallholder communities of six sociolinguistic groups (Akha, Bulang, Han, Hmong, Lahu, and Yao) that manage tea resources in forests, agro-forests, mixed crop fields, and terrace gardens. Interviews were carried out between 2006 - 2010 to identify the influence of socio-economic and policy variables on tea production and consumption patterns. Ecological plot sampling and ethnobotanical inventories were employed to characterize the composition, structure, and uses of tea management systems. Tea leaf samples were randomly selected within each plot for: (1) video morphometrics to measure six shape and size attributes, (2) high performance liquid chromatography (HPLC) to quantify nine catechin and methylxanthine compounds and, (3) amplified fragment length polymorphisms (AFLP) molecular marker analysis to assess genetic diversity. Results indicate a relationship between the perceived value of a commodity and a change of management practices, ecological knowledge, and land use. Findings demonstrate how variable management practices result in the loss, conservation, or enhancement of plant species richness and genetic diversity, and how smallholders variably benefit from diversity in their agro-ecosystems. Plant species richness was found in the order agro-forest edge > forest > agro-forest > mixed crop field > terrace gardens. Statistically significant variation was found in morphological, phytochemical, and genetic characters between the different types of tea management systems. Morphological diversity was found in the order agro-forest > mixed crop field > forest > terrace gardens, whereas genetic diversity was found in the order mixed crop field > agro-forest > forest > terrace gardens. HPLC data show that tea samples from agro-forests and mixed crop fields had greater mean Total Catechin Content (TCC) and mean Total Methylxanthine Content (TMC) compared to forests and terrace gardens. Results further demonstrate that management, processing, and preparation methods are related to the phytochemical profile, anti-oxidant activity, and flavor of tea. This study provides useful baseline data to examine long-term change linked to expanded market integration and an engagement of ecosystem ecology with anthropology.

  • MAG does not Require NgR1, PirB or Sialic Acid Binding to Inhibit Neurite Outgrowth

    Author:
    Najat Al-BASHIR
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Marie Filbin
    Abstract:

    The Role of Gangliosides, NgR1, NgR2 and PirB Receptors in MAG Inhibition of Neurite Outgrowth by Najat Al-bashir Thesis Advisor: Dr. Marie T. Filbin Following injury, axons in the central nervous system (CNS) do not spontaneously regenerate, and this is due to several factors, one of which is the presence of myelin- associated inhibitors. There are three major myelin-associated inhibitors that have been identified, Nogo-66, myelin associated glycoprotein (MAG), and Oligodendrocyte myelin glycoprotein (OMgp). MAG is a member of immunoglobulin (IgG) super-family and contains 5 Ig-like domains in its extracellular domain. Like Nogo-66 and OMgp, MAG binds to a receptor complex consisting of NgR1- p75NTR-Lingo-1 to inhibit neurite outgrowth. MAG is also a sialic acid binding protein and specifically binds to gangliosides GT1b and GD1a. Recently, NgR2 was also shown to be a sialic acid- dependent binding receptor for MAG. Recently, paired immunoglobulin B (PirB) was also identified as a novel receptor for MAG, Nogo-66 and OMgp. Previously, we showed that the sialic acid binding activity of MAG is not necessary for its inhibitory effects. We mapped the sialic acid binding site on MAG to Arg 118 in the first Ig-domain. When this site is mutated, sialic acid binding is lost but MAG, when expressed by CHO cells, still retains its ability to inhibit neurite outgrowth. Also, we showed that a soluble form of MAG consisting of the MAG extracellular domain fused to the Fc portion of human IgG (MAG-Fc), and a truncated soluble form of MAG consisting iii only of the first three Ig-like domains (MAG (d1-3)-Fc), both bind to neurons in a sialic acid-dependent manner; however, only MAG-Fc inhibits neurite outgrowth. In addition, MAG mutated at Arg118 (MAG (R118A)-Fc), does not bind to neurons and could not inhibit neurite outgrowth. Recently, we mapped the inhibition site on MAG to Ig-domain 5, which is distinct from the sialic acid binding site. Others have reported that gangliosides are functional binding partners for MAG and are necessary for inhibition by MAG when expressed in immobilized membranes. They reported that neurons from mice deficient in the B1, 4-N-actylgalactosaminyltransferase (GalNAcT) gene, which lack all complex gangliosides including GT1b and GD1a, are not inhibited by MAG in immobilized membrane. Others have also shown that clustering gangliosides with antibodies in the absence of MAG is sufficient to inhibit neurite outgrowth via a mechanism engaging p75 NTR receptor. Here we show that clustering MAG (d1-3)-Fc can inhibit neurite outgrowth in neurons from wild type mice but not from GalNAcT deficient mice. We also show that MAG can inhibit neurite outgrowth independent of NgR1, PirB, and sialic acid binding. We show that neurons from GalNAcT deficient mice are inhibited by MAG as effectively as neurons from wild type mice. Also, we show that neurons from NgR1 deficient mice are inhibited by full length MAG and mutated MAG (MAG R118A) that cannot bind sialic acid residues. In addition, in the presence of PirB antibodies, both MAG- and mutated MAG (R118A)-expressing CHO were able to inhibit neurite outgrowth of neurons from NgR1 deficient mice and wild type mice. Taking all these results together, MAG interacts with another as yet unknown receptor(s), in addition to NgR's, PirB and sialic acid to inhibit neurite outgrowth.

  • Neural Effects of Exposure to the Environmental Chemical, Bisphenol A, During Development

    Author:
    Ayanna Alexander
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Victoria Luine
    Abstract:

    Exposure to Bisphenol A (BPA), an environmental chemical, has been linked to changes in physiology, neural development, and behavior. The focus of this study was to determine the effects of BPA exposure, during a short developmental window, on physiology, activity, anxiety, cognition, and neurochemistry. In prenatal study, dams were administered 100 mcg/kg/day orally, from gestational day 16 to parturition. Postnatal study pups received subcutaneous injection of 60 or 100 mcg/kg BPA from postnatal day 0 to 6. All pups were weighed, examined for evidence of vaginal opening, and, at adulthood, performed behavioral tasks measuring locomotor activity, anxiety, and visual and spatial memory. Brain monoamines were measured using high performance liquid chromatography in the postnatal group. Prenatal BPA contributed to low juvenile body weight in both sexes and adult overweight in male subjects. Hyperactivity and memory deficits were observed in both sexes of BPA treated subjects. Postnatal 100 mcg/kg BPA females experienced delayed vaginal opening, less anxiety behavior in elevated plus maze, and spatial memory impairments. BPA treated subjects of both sexes had increased norepinephrine and dopamine turnover in basolateral amygdala and hippocampus, areas which are implicated in anxiety and cognition, respectively. The data suggests that BPA exposure during perinatal life causes disruptions in physiology, behavior, memory and neurochemistry that persist to adulthood. In addition, postnatal effects of BPA may be mediated by alterations in central monoaminergic function.

  • The Vocal Behaviors of Captive North American River Otters (Lontra canadensis) Individual differences and shared repertoires

    Author:
    Carla Almonte
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Richard Veit
    Abstract:

    The current information on the vocal repertoire of the North American River Otter is very limited. To date there have been no direct studies conducted on their repertories. In this study, I examined the vocal behavior of 12 captive river otters. The discriminant function analysis suggests that river otters have 4 distinct call types with 7 sub-call types and one call the whistle is unique to one group of pups. The results of the Kruskal-Wallis comparing acoustical structures shows strong evidence for the presence of individuality with some individuals showing greater differences in comparison to the others. I also examined the differences in sexes and age groups, and the results show that unique calls are present, and there are significant differences across groups when comparing acoustical structures. Finally, I examined the uses of vocalizations, and the results show a positive correlation between the duration, max frequency, and max power of the call and the arousal state of the individual producing the call. Specific call types also showed tendencies to be produced when the individual was in a particular interaction (asocial or social) and when in a particular arousal state.

  • The Ecology of the Woodlands of Central Park, New York City

    Author:
    Regina Alvarez
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Dwight Kincaid
    Abstract:

    A quantitative ecological inventory was conducted in the 54.6-hectare (ha) urban woodlands of Central Park, New York City. Fifteen sites were selected and woody stems greater than or equal to one centimeter (cm) diameter were surveyed using the point-centered quarter transect method. Total area surveyed was 1.091 hectares. The survey tallied 1,271 stems from 82 species in 31 families and 50 genera. Stem diameters ranged from 1 cm to 218 cm. In terms of ecological dominance, Prunus serotina Ehrh. was the dominant taxon followed by Quercus rubra L. The largest trees were Quercus rubra, Prunus serotina, Morus alba L., Phellodendron amurense Rupr., Platanus occidentalis L., Liriodendron tulipifera L., Quercus palustris Münchh., Ulmus americana L., and Styphnolobium japonicum (L.) Schott, ranging in diameter from 100 cm to 218 cm. Lower diameter at breast height (DBH) quartile stem sizes were dominated by Acer platanoides L., Prunus serotina, Celtis occidentalis L. and Q. palustris. As a fully human-made park under continual management, these woodlands contain a high percentage of non-native and horticultural species. A survey of the biodiversity of the park, however, shows the significant role even a highly managed park can play in wildlife habitat. Invasive plants are a serious threat to native plants and wildlife habitat everywhere. Numerous invasive species are present in Central Park. This study evaluates management practices to control these species and makes further recommendations. It analyzes the potential of other non-native species, as well as native species, to become invasive. This study can help park managers decide which plants to highlight and preserve and which to manage and control.

  • The diet and foraging ecology of gray seals, Halichoerus grypus, in United States waters

    Author:
    Kristen Ampela
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Richard Veit
    Abstract:

    Once extinct in U.S. waters, there are now more than 7,000 gray seals (Halichoerus grypus) that breed and forage in the waters of Maine and Massachusetts. This is the first long-term study of the diet and foraging behavior of this species in its U.S. range. I used hard parts in 305 seal scats and 49 stomachs, and fatty acid profiles in 45 seal blubber cores, to 1) reconstruct the diet of gray seals in U.S. waters, and 2) investigate regional, temporal, and intraspecific variation in the diet. I compared species in the diet with those most abundant in the seals' range, as measured by bottom trawl surveys. I analyzed the tracks of 6 satellite-tagged seals, and asked which prey species were most abundant in areas where foraging activity occurred. I recovered a total of 3,798 otoliths, and 7,005 prey individuals from 34 prey taxa. Sand lance (Ammodytes spp.) dominated the diet by weight (53.3% of total) and number (66.3% of total). Sand lance, winter flounder (Pseudopleuronectes americanus), red/white hake (Urophycis spp.) and Atlantic cod (Gadus morhua) together made up 82% of the diet by weight. Cod comprised 6.4% of the diet by weight, although this varied seasonally. Fatty acid profiles were best able to classify seals by age (young-of-the-year pups vs. yearlings, Wilks-Lambda = 0.27, F25,19 = 2.07, p <0.054), suggesting that diet differences were most pronounced between these two groups. Consistent 2:1 ratios of 22:6n3 and 20:5n3 fatty acids occurred in seal blubber (10.12/5.00 = 2.02). These ratios are similar to those in smooth skate (Malacoraja senta, 20.87/10.02 = 2.08) and alewife (Alosa pseudoharengus, 15.04/7.48 = 2.01), indicating that these species were important in the diet. Seals consumed abundant species, and tracked interannual trends in sand lance abundance, but the diet could not be predicted from prey availability alone. Satellite telemetry of seals revealed area restricted search behavior and central place foraging activity in areas with high abundance of sand lance and winter flounder, and these taxa comprised over 72% of the diet estimated from scats.

  • Neuromodulatory and cytoprotective roles of zinc in the vertebrate retina

    Author:
    Ivan Anastassov
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Richard Chappell
    Abstract:

    There is increasing evidence that the role of Zn2+ in the central nervous system is more complex and widespread than originally thought. Chelatable Zn2+ is co-localized with glutamate in the terminals of mossy fiber hippocampal and first order retinal neurons. The co-release of Zn2+ with glutamate in a stimulation-dependent manner has been shown in the hippocampus and the distal retina, while the electrophysiological effects of photoreceptor-released Zn2+ suggest a neuromodulatory role at the first visual synapse. This dissertation examines the neuromodulatory and cytoprotective roles of zinc in the vertebrate retina. When endogenous Zn2+ release is chelated in a skate eyecup preparation, the photoreceptor-generated a-wave of the electroretinogram doubles. This treatment also depolarizes horizontal cells and enhances their light response, suggesting that in the absence of Zn2+ , tonic release of glutamate from photoreceptors onto postsynaptic neurons is increased. Live cell imaging demonstrates that Zn2+ is released from photoreceptor terminals following Ca2+ entry through synaptic voltage-gated calcium channels. In isolated photoreceptors from salamander, chelation of extracellular Zn2+ significantly increases Ca2+ entry at the terminal and this effect is abolished when voltage-gated calcium channels are blocked pharmacologically. In the skate, removal of retinal Zn2+ via intraocular injections of chelators severely damages the inner retina. In the absence of Zn2+ , the retina develops classic signs of glutamate excitotoxicity; cell and tissue swelling, pyknosis and spongy appearance of the inner plexiform layer. Similar tissue characteristics are observed with injections of kainate, a well-known and potent excitotoxic agent. Additionally, neurons in the ganglion cell layer become necrotic with either kainate or chelator treatments, suggesting they are particularly sensitive to overactivation of glutamate receptors. Taken together, these experiments show the importance of Zn2+ as a neuromodulatory agent at the first visual synapse, where control of glutamate release affects the transmission of the visual message and provides broad protection of the retina from excitotoxicity. Understanding the role of Zn2+ in the retina may provide novel insights into retinal diseases and contribute to our growing knowledge of zinc's important functions elsewhere in the CNS.

  • MOLECULAR PHYLOGENETICS OF OTOPHYSAN FISHES: AFRICAN ALESTIDS (CHARACIFORMES: ALESTIDAE) AND CITHARINOIDS (CHARACIFORMES: CITHARINOIDEI), AFRO-ASIAN CHEDRINS (CYPRINIFORMES: CHEDRINI), AND NEOTROPICAL LORICARIINS (SILURIFORMES: LORICARIINAE) AS CASE STUDIES

    Author:
    Jairo Arroyave Gutiérrez
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Scott Schaefer
    Abstract:

    Otophysan fishes (Ostariophysi: Otophysi) are members of a morphologically and ecologically diverse clade of teleosts that includes most freshwater species of fish, and comprises four major lineages classified in the orders Cypriniformes, Characiformes, Siluriformes, and Gymnotiformes, respectively. Partly because of their tremendous diversity, many groups of otophysan fishes remain poorly understood phylogenetically and in a state of taxonomic disarray. This is the case--to a greater or lesser extent--of African characiforms of the suborder Citharinoidei and the family Alestidae, Afro-Asian cypriniforms of the tribe Chedrini, and Neotropical siluriforms of the subfamily Loricariinae. To address the lack of robust, comprehensive, and/or up-to-date phylogenetic hypotheses for the aforementioned groups, this doctoral dissertation investigated their systematics and evolution through phylogenetic analyses of comparative DNA sequence data, including molecular-clock analyses that resulted in the first time-calibrated phylogenies ever proposed for both alestids and citharinoids (and characiforms for that matter). The molecular phylogenies arrived at herein represent the most comprehensive hypotheses of relationships for each of the groups investigated. Although many of the relationships revealed by this study corroborated previous hypotheses based on morphological and/or molecular data, others are newly hypothesized or in conflict. Moreover, the results of this research revealed instances of para- and polyphyly in numerous nominal taxa (e.g., Brycinus [Alestidae], Nannocharax [Distichodontidae], Raiamas [Chedrini], Lamontichthys [Loricariinae]), prompting a reassessment of the taxonomies of the groups investigated. Information on the temporal context of alestid and citharinoid diversification was used to assess biogeographic hypotheses proposed to explain the Gondwanan distribution of characiforms. Likewise, the inferred chronograms shed some critical light on the historical processes that may have influenced diversification and biogeographic patterns in these and other groups of African freshwater fishes.

  • Population Genetics of Canine Heartworm (Dirofilaria immitis)

    Author:
    Diana Belanger
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Robert Rockwell
    Abstract:

    Dirofilaria immitis, canine heartworm, is a filarial nematode that may have genetic features that favor the development of drug resistance, including rapid rates of mutation, large population sizes, and high levels of gene flow. This parasite is currently treated with macrocyclic lactone anthelminthics, and while it has not yet shown evidence for evolving resistance to these chemotherapeutic compounds, resistance has evolved in related filarial nematodes infecting ruminants and humans. Heartworm samples from domestic dogs and coyotes were obtained via donations from veterinarians and researchers across the United States. I isolated and characterized 11 microsatellite loci for canine heartworm. Using the observed distribution of alleles, I determined the amount of genetic variability and quantified the partitioning of genetic variance. In conjunction with microsatellite data, specific mitochondrial (cox1) and Wolbachia (wsp and ftsZ) loci were used to genotype a subset of host taxa. Results indicate a lack of mitochondrial diversity and maximum likelihood trees show no discernable geographic patterning on a continental scale. This is not unexpected in a Wolbachia-infected organism like D. immitis as this bacterium has been shown to purge mitochondrial diversity in numerous model systems. After establishing baseline genetic parameters, a model of population dynamics was created to answer questions about the potential spread of drug resistance alleles. In the absence of selection, gene flow between subpopulations drives the dispersal of drug resistance alleles. Fixation time is directly proportional to selection pressure. When resistance alleles arise in a source population they spread more rapidly than if they arise in a sequestered population.

  • Microspherule Protein Msp58 and Ubiquitin Ligase EDD Form a Stable Complex that Regulates Cell Proliferation

    Author:
    Mario Benavides
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Hualin Zhong
    Abstract:

    A complex molecular network is put into place at specific phases of the cell cycle to prevent unscheduled cell division that could result in malignant cell growth. Emerging evidence shows that still uncharacterized proteins play crucial functions at those cell cycle transition points. Nuclear protein Msp58 and EDD E3 ubiquitin ligase have been implicated in different aspects of cell proliferation and reported to be abnormally expressed in numerous types of cancers. The molecular mechanisms underlying Msp58 and EDD functions, however, are not well understood. The work presented here shows that Msp58 and EDD form a stable protein complex that regulates cell viability and proliferation. Interestingly, knockdown of EDD by RNA interference leads to a significant accumulation of Msp58 protein, which suggests that EDD serves as a negative regulator of Msp58. In addition, our in vivo ubiquitination assays and analyses of various cell lines treated with translational and proteasomal inhibitors demonstrate that Msp58 is regulated post-translationally by the ubiquitin-proteasome pathway. These results imply that EDD ligase activity is involved in this regulatory process. Using flow cytometry analyses and biochemical characterization of Msp58 and/or EDD depleted cells, we show that the Msp58-EDD complex plays important roles in cell cycle progression via the control of cyclin gene expression. In particular, silencing Msp58 and/or EDD alters the protein levels of cyclins B, D and E. Taken together, our data suggest that a set of the biological roles attributed to Msp58 and EDD may be executed in the context of the complex that they form, thereby revealing a novel molecular mechanism for these two proteins to accomplish their functions.