Alumni Dissertations

 

Alumni Dissertations

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  • Chemical, genetic, and ethnobotanical diversity in Asian eggplant

    Author:
    Rachel Meyer
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Amy Litt
    Abstract:

    Eggplants (Solanum melongena L.) were domesticated in tropical Asia where they are used abundantly as both food and medicine. Human selection has produced hundreds of landraces that differ in morphology and chemistry in ways that may be related to local ethnobotanical preferences. Here I present a study of the genetic, phytochemical, and ethnobotanical diversity of Asian eggplant landraces and wild relatives, which together aimed to identify the molecular and chemical differences among lineages, correlate these differences with domestication and possible selection pressures, and generate hypotheses about shifts in gene regulation that could have caused these differences. Phylogeographic analyses revealed that eggplants were domesticated at least three times, in India, southern China, and the Indo-Malayan islands (Malesia). Interviews and literature review of contemporary and historic ethnobotanical data on eggplant from India, China, and Malesia, revealed largely different medicinal uses of eggplant among these regions, suggesting separate domestications could have produced fruit with different phytochemistry. Analyses of eggplant chemical profiles spanning 43 phenolic compounds, many of which have therapeutic and flavorful qualities, were compared to genetic and geographic data. Results showed that these putatively independently domesticated lineages have significantly different levels of hydroxycinnamic acid polyamine amides, which actually may contribute to fruit texture and size, in addition to health beneficial qualities of the fruit. Analyses also revealed all three domestication events produced eggplants with lower total phenolic abundance, suggesting milder flavor was preferred that lowered health beneficial compounds. Study of genes expression levels of 13 enzymes in the phenolic pathway revealed that differential expression of six genes may underlie the different phytochemical profiles; these genes encode spermine and spermidine hydroxycinnamoyl transferases, hydroxycinnamoyl transferase, and cinnamoyl 3- hydrolase. These studies allowed me to propose detailed routes of phenolic biosynthesis in eggplant, and suggest that expression levels of these potential key regulatory genes of hydroxycinnamic acid synthesis were altered during the domestication process in multiple centers of domestication.

  • The Role of Serotonin 1A Receptor-Mediated Signaling in PSD95 Induction and Synaptogenesis During Neonatal Hippocampal Development

    Author:
    Amit Mogha
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Probal Banerjee
    Abstract:

    Previous studies have shown that the 5-HT1A-R is essential for neonatal front brain development. A polymorphism in 5-HT1A-R gene leading to its aberrant expression has been reported to result in severe depression in humans, while its absence up to postnatal day 15 (P15) results in anxiety like behavior in mice. How this receptor functions to regulate the behavior of an animal is still poorly understood. Our prior studies have shown that 5-HT1A-R mediated signaling pathway leads to stimulation of a neuro-protective MAPKèPKCα pathway in differentiated hippocampal neuron-derived HN2-5 cells. Further studies showed that this pathway is also functional in cultured P15 hippocampal slices and that it causes an induction in field EPSP (fEPSP) in the P15 slices. To further understand the mechanistic role of 5-HT1A-R in synaptogenesis we used organotypic hippocampal slice cultures from C57BL6 mice at P15 to show that the activation of 5-HT1A-R mediated signaling pathway in the hippocampus leads to a massive increase in PSD95 expression and dendritic spine as well as synapse number. The results presented in our study demonstrate that 5-HT1A-R mediated signaling pathway acts via sequential activation of ERK and PKC. In vivo studies by intrahippocampally infusing 5-HT1A-R agonist and different signaling inhibitors revealed that the same pathway is involved in the induction of PSD95 and synaptogenesis in vivo via activation of PKCα in C57 as well as Swiss Webster mice. We further demonstrated that intra-hippocampal infusion of antidepressant drug like Fluoxetine, which is Selective Serotonin Reuptake Inhibitor (SSRI), leads to the induction of PSD95 and synaptogenesis through the same pathway. Equipped with this knowledge, we activated the 5-HT1A-R mediated signaling pathway in 5-HT1A-R (-/-) mice by activating the downstream effector PKCα by intrahippocampally infusing its activator Bryostatin, which is also an Alzheimer's drug, to boost PSD95 expression and synaptogenesis. We also observed that the 5-HT1A-R (-/-) mice have less number of synapses in the hippocampus. We, therefore for the first time elucidate the signaling pathway which explains how 5-HT1A-R regulates hippocampal sculpting and function, which may determine the affective normalcy of an adult.

  • Production of Phenolic Diterpenes in Tissue Culture of Rosmarinus officinalis L.

    Author:
    Kiyo Mondo
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Dominick Basile
    Abstract:

    Rosemary (Rosmarinus officinalis L.) is an herb native to the Mediterranean that has been used to prevent the oxidation of fats and oils in foods and cosmetics. The leaves of rosemary are a powerful source of natural antioxidants; the potent antioxidant properties of its extracts are mainly due to the phenolic diterpenes, carnosol and carnosic acid. At present, field-grown plants are the sole source of carnosic acid and carnosol. Rosemary is relatively easy to grow in many parts of world; however the variation of seasonal stresses such as temperature, solar irradiation, and rainfall can significantly alter the level and quality of phenolic diterpenes. An alternative method with more consistent results to obtain phenolic diterpenes from rosemary is a biotechnological approach, specifically, plant tissue culture. In this research, different culture types (callus cultures, suspension cultures, and shoots from in vitro propagated plants) of rosemary were established, and the effects of temperature, light intensity, and UV radiation for enhancing the synthesis of carnosic acid, carnosol, and related phenolic diterpenes in these cultures were evaluated. MS medium supplemented with either 10 mg/L indole-3-acetic acid (IAA), 4 mg/L benzylaminopurine (BAP) and 1 mg/L 6-furfurylaminopurine (kinetin) or 0.05 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.5 mg/L BAP at 18 and 25°C with 67.5 to 81.0 µmol m-2s-1 proved to be the best medium and conditions for developing and sustaining rosemary callus cultures. Shoots from in vitro regenerated plants of rosemary accumulated various amounts of carnosic acid and carnosol, which were also present in callus culture, but the yields of these compounds were considerably lower than in regenerated shoots or in dried field grown leaves. Only carnosol and rosmanol, not carnosic acid, were detected in cell aggregates in suspension cultures, whereas spent medium contained only rosmanol. Exposure of the callus cultures to several stress conditions by increasing temperatures and light intensities, and UV radiation treatments enhanced the level of the phenolic diterpenes, carnosic acid and carnosol.

  • The Liochelidae Fet & Bechly, 2001 (Scorpiones) of the Indo-Pacific Region: systematics and biogeography

    Author:
    Lionel Monod
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Lorenzo Prendini
    Abstract:

    The aim of the present project was to reassess the systematics, phylogeny and biogeography of the Indo-Pacific taxa of the scorpion family Liochelidae Fet & Bechly, 2001 based on morphology and molecules. The morphological matrix comprised of 85 terminal taxa and 263 characters was compiled based on the examination of more than 4000 specimens including most of the types and fresh material collected during several field surveys in Australia, Malaysia, New Caledonia, the Solomon Islands and Thailand. 101 DNA samples representing 42 taxa, half of the known diversity, were obtained for the molecular analysis. Three mitochondrial and two nuclear genes (approximately 4180 base-pairs) were sequenced from each sample. Cladistic analyses were then performed on the morphological, the molecular and the combined datasets respectively. Finally, dates of cladogenesis events estimated using molecular clocks were used to infer a plausible biogeographical hypothesis. Results of the taxonomic revision lead to the following emendations: (1) the elevation of the subfamily Hormurinae Laurie, 1896 to family level, (2) the revalidation of Hormiops Fage, 1933 and Hormurus Thorell, 1876 that were placed into synonymy with Liocheles Sundevall, 1883, (3) the revalidation of 10 species placed into synonymy (eight Hormurus spp., two Liocheles spp.), (4) the discovery of 51 new species (1 Hormiops, 48 Hormurus, 1 Liocheles, 1 Opisthacanthus Peters, 1861 (Monodopisthacanthus Lourenço, 2001)), (6) the elevation of two subspecies to species rank, and (5) the synonymy of one genus (Tibetiomachus Lourenço & Qi, 2006), three species and one subspecies. The biogeographical analysis indicates that vicariance, dispersal and vicariance are not mutually exclusive and that all three mechanisms played a significant role in the development of the Indo-Pacific liochelids. The phylogeny and dating do not corroborate the "out-of- India" origin for the Southeast Asian taxa, but rather suggest that they may be part of an ancient Laurasian lineage. On the other hand, the colonisation of the Australo-Papuan Archipelago from Sundaland by liochelids is confirmed. However, the age estimate of divergence between Melanesian Hormurus and Asian Liocheles in the Paleocene contradicts the current geological model and suggests the existence of land connections between the two provinces well before the Eocene.

  • ECOLOGY OF A SOUTHWEST NEW ENGLAND FOREST AND ITS INVASION BY A NON NATIVE TREE SPECIES

    Author:
    Eric Morgan
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Dwight Kincaid
    Abstract:

    With the regeneration of vast forested areas in northeastern North America, a renewed interest in studying these recovering areas has arisen in recent years. The process of accurately inventorying existing forested areas and applying statistical methods to recognize forest types and plant associations has become an important aspect of modern ecological study. While forest change is a natural process and each forest has its own individual mosaic of species, the documentation of species within these areas will allow changes to be recognized more accurately, and earlier than in years past. Using a 31 hectare forest located in southwest Connecticut as a research site, an annotated flora of all non vascular and vascular plant species was conducted. Results included 71 non vascular and 357 vascular species being recorded and vouchered. Vegetation analyses of the site were performed through the use of 10 x 10m quadrats. This analysis showed a forest dominated by Fagus grandifolia followed by Acer rubrum and Betula lenta. Four distinct forest types exist with a mixed hardwoods forest type dominating. A non native species, Phellodendron amurense was recognized as being the 14th most dominant in importance value ranking. Sites were then identified within the forest to locate areas of high concentration of the species, and within the largest of these areas a comprehensive examination of the invasion was performed. An analysis of the age structure, impacts upon the understory, and pattern of the invasion were investigated by creating a large plot encompassing all the P. amurense and gathering cartesian coordinates, diameter at breast height, and age from tree ring analysis. The results of this thesis provide an accurate and thorough inventory of all non vascular and vascular plants on the site. Furthermore, an examination of the forest types and importance values of the area provide an even better baseline from which future analysis may be based. This thesis also provides significant information regarding a non native invasive species that is currently not recognized as such in much of the pertinent literature.

  • Phenolic Constituents from Garcinia intermedia and Related Species

    Author:
    Ulyana Munoz Acuna
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Edward Kennelly
    Abstract:

    Antioxidants from plants scavenge free radicals and prevent reactive oxygen species from having damaging effects in common ailments such as inflammation, atherosclerosis, and Alzheimer's disease. As part of our ongoing studies of antioxidants from tropical edible fruits, we have studied Garcinia intermedia (Pittier) Hammel [synonym: Rheedia edulis (Seem.) Planch. & Triana], native to Central America. In the fruits the following compounds were identified: guttiferone A, guttiferone E, xanthochymol, fukugetin, volkensiflavone and fukugeside. A new compound was tentatively identified in the fruits of this species. The antioxidant activity of guttiferone A in the 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay was IC50 = 46 µM. The antiproliferative effect of guttiferone A against colon cancer cells (HT-29) was IC50 = 15.8 µM. A reversed-phase high-performance liquid chromatography (RP-HPLC) method with diode array detection (DAD) was developed and validated to quantify seven major phenolic compounds in eight Garcinia species from different geographic regions: G. mangostana, G. xanthochymus, G. spicata, G. livingstonei, G. intermedia, G. hombroniana, G. kola, and G. aristata. Garcina intermedia and G. mangostana had the highest antioxidant activities.

  • POPULATION DYNAMICS OF THE AMERICAN OYSTERCATCHER (HAEMATOPUS PALLIATUS) NEAR THE NORTHERN LIMIT OF ITS RANGE

    Author:
    Sean Murphy
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Richard Veit
    Abstract:

    American Oystercatchers (Haematopus palliatus) expanded their range north along the Atlantic Coast, reaching Massachusetts 40 years ago. Concurrent to northward range expansion, oystercatchers have declined in the core part of their range, and have been designated a "Species of High Concern" by the U.S. Shorebird Plan. I examined the demographics of a migratory population of American Oystercatchers in Nantucket, Massachusetts to explore factors influencing local populations. I estimated fecundity (0.20 females fledged per female), annual survival, and dispersal using a variety of field and statistical techniques. I analyzed data from four nesting seasons for oystercatchers in Nantucket and examined temporal patterns in reproductive success. All my measures of reproduction were higher than those from other Atlantic Coast populations. I hypothesized that island populations experience higher reproductive success due to the absence of mammalian predators, and these populations may be sustaining mainland populations. Furthermore, I found that egg survival was exceptionally high but chick survival was low. Therefore, identification of chick loss should be a priority in conservation efforts. I used advanced mark-recapture techniques to estimate annual adult survival and breeding-site fidelity for American Oystercatchers. My results revealed a high rate of true annual survival (0.94) and a strong, but variable, degree of breeding-site fidelity (0.93). Additionally, I used mark-recapture data to estimate juvenile annual survival (0.51) and subadult transition probability (0.18). Using perturbation analyses, I found adult survival and breeding-site fidelity had the greatest impact on local population growth. My modeling also indicated that current reproductive success is sufficient to maintain the population (λ=0.970, 95% CI: 0.90 - 1.02), but not sufficient to predict the recent increase. Using reverse encounter histories, I estimated movement parameters and found approximately 7% of the population permanently emigrates while 16% of the population is likely comprised of adults immigrating into Nantucket. Demographic analyses confirmed that high immigration rates are responsible for the observed growth (λ = 1.08, 95% CI: 0.99 - 1.16). My dissertation provides a foundation for continued examination of shorebird population demographics, a model for demographic analyses of a species of conservation concern, and a preliminary work illuminating the advantages of dispersal and the relationship between breeding-site fidelity and reproductive success.

  • UBIQUITIN PROTEASOME PATHWAY, AUTOPHAGY AND A NOVEL THERAPEUTIC APPROACH TO PREVENT NEURODEGENERATION LINKED TO INFLAMMATION IN ALS

    Author:
    Natura Myeku
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    MARIA FIGUEIREDO-PEREIRA
    Abstract:

    Neurodegenerative disorders such as Alzheimer's, Parkinson's and Huntington's diseases as well as amyotrophic lateral sclerosis (ALS), are a heterogeneous group of clinical disorders characterized by the selective loss of neurons in specific regions of the CNS. Despite their variability they have similar features including the accumulation of proteins that develop into inclusion bodies. Ubiquitinated proteins are major components of these inclusions suggesting that impaired proteasome activity and/or dysfunction of the ubiquitination pathway may be main players in this process. Emerging data reveal that autophagosomes are also components of inclusion bodies, implicating autophagy in neurodegenerative disorders as well. The research described in this thesis led to two discoveries: 1) The UPP, not autophagy, is the main pathway implicated in the degradation of soluble ubiquitinated proteins. Furthermore, proteasome impairment, and not autophagy dysfunction, causes the intracellular accumulation/aggregation of ubiquitinated proteins. We demonstrate that proteasome impairment leads to accumulation of ubiquitinated proteins. Most importantly, inhibition of autophagy failed to cause ubiquitin protein accumulation. We also established that the soluble p62/sqstm1, a polyubiquitin shuttling factor, is associated with the proteasomes and not with autophagosomes. It is thought that p62/sqstm1 delivers polyubiquitinated proteins to proteasomes and/or autophagosomes for degradation. From a therapeutic point of view our data support the notion that pharmacological means to sustain or enhance proteasome activity and p62/sqstm1 levels could be an efficacious strategy to remove ubiquitinated proteins and prevent or delay the onset of neurodegeneration associated with protein aggregation. 2) The activity of the proteasome and the levels of p62/sqstm1 are significantly enhanced by dibutyryl-cAMP in spinal cord cultures. We demonstrate that db-cAMP enhances the activity of the proteasome and p62/sqstm1 levels. Furthermore, pre-treatment of the neuronal cultures with db-cAMP mitigate cell toxicity induced by prostaglandin J2 (PGJ2). PGJ2 is an inflammatory mediator found to be elevated in post mortem slices of spinal cord motor neurons in ALS patients. Our data support the notion that enhancing of proteasome activity by the cAMP/PKA pathway provides an effective neuroprotective strategy against ALS and other neurodegenerative diseases associated with proteinaceous aggregates and signs of neuroinflammation. In conclusion, our data support that impaired proteasome activity occupies the center stage in the development of neurodegenerative diseases. Enhancing proteasome activity can have therapeutic implications in drug development aiming at prevention and treatment of neurodegenerative disorders.

  • POPULATION DYNAMICS AND OCCUPANCY PATTERNS OF EASTERN SCREECH OWLS (MEGASCOPS ASIO) IN NEW YORK CITY PARKS AND ADJACENT SUBURBS

    Author:
    Christopher Nagy
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Robert Rockwell
    Abstract:

    Eastern screech owls (Megascops asio) are one of the few raptor species that permanently reside in New York City (NYC). To better inform management of this charismatic species in urban parks, I sought to determine the present status and future viability of existing screech owl populations in NYC and identify potential landscape characteristics that affect park occupancy by screech owls. Using captive, non-releasable owls and isolated free-living owls, I developed a method of identifying individual screech owls via vocalization analysis. Using call-broadcast surveys and subsequent recording of owl responses, I gathered capture-recapture histories of urban owls in three NYC parks and one comparison nature preserve, the Mianus River Gorge Preserve (MRGP), a rural/suburban nature preserve in Bedford, NY. These histories were used to estimate abundance and survival rate in each of the parks. I then projected simulated populations using my estimated adult survival and previously published yearling survival and reproductive rates. I built my projection model to include density dependence based on park area, realistic sex ratio fluctuations, and periodic drops in survival rate due to hypothetical environmental events. Survival in urban parks was 0.98 - 1.0, much greater than in the MRGP, 0.57 ± 0.15. Despite the high adult survival, populations in parks could be extirpated within 10 - 20 years by severe drops in survival rate (e.g., extreme winters, storms, or secondary poisoning) if such conditions occurred more often than once every ten years or if parks were smaller than 1.0km2. In 2008 and 2009, my colleagues and I conducted a citizen science-based study on screech owl occupancy patterns across three counties adjacent to NYC: Westchester and Putnam, NY, and Fairfield, CT. Volunteers conducted call-broadcast surveys on their own properties and sent my colleagues and me the results in 2008 and 2009. Occupancy and detection were modeled as functions of the amount of forest cover and impervious surface cover at each survey point. These models were validated against an independent dataset collected by myself and other trained scientists. Validated models indicated a negative association between occupancy and percent forest cover or, similarly, a positive association with percent impervious cover. Both the citizen science and the systematic datasets supported similar owl-habitat patterns of higher occupancy probabilities in developed areas compared to rural. The above patterns described eastern screech owl habitat use in rural and suburban areas outside of NYC. I hypothesized that at some point urbanization would become too intense for owls to tolerate, and they would be primarily relegated to protected greenspaces in extremely urbanized cities, as I observed in NYC. In 2010, I surveyed 13 additional parks in NYC and the more urban southern sections of Westchester to characterize occupancy patterns in highly urban areas. I used similar landscape measurements as in the citizen science study, only these measurements were taken across the entire park. Occupancy appeared to decline sharply if the percent impervious cover surrounding a park rose above 50 - 60%. I interpreted this pattern as evidence that high urbanization around a park acts primarily as a barrier to immigration. It is also possible that high urbanization around a park leads to higher mortality from vehicles. In terms of management, my work has indicated that in large parks (e.g., >1km2), extinction probability is relatively low, but parks larger than 3km2 may be less suitable if big parks allow the establishment of larger raptors such as barred (Strix varia) or great horned owls (Bubo virginianus). Managers can enhance population persistence by increasing the amount of available habitat via habitat restoration and reforesting or re-meadowing developed but unused parks (e.g., large lawns and paved areas) and increasing over-winter survival and reproductive rates by installing nest boxes. However, frequent chance events can extirpate any park-bound population, and thus managers and city planners should also look to enhance the probability of dispersal and recolonization via corridors or reducing the general level of urbanization around protected parks.

  • THE CHARACTERIZATION OF Pb2+ TOXICITY IN RAT NEURAL DEVELOPMENT: AN ASSESSMENT OF Pb2+ EFFECTS ON THE GABA SHIFT IN NEURAL NETWORKS AND IMPLICATIONS FOR LEARNING AND MEMORY DISRUPTION

    Author:
    Lorenz Neuwirth
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    Abdeslem El Idrissi
    Abstract:

    The toxic effects of Pb2+ on the developing rat nervous system has been investigated to assess early developmental GABAergic disruption and its implications with altering inhibitory learning and memory. This goal was achieved using a multi-systems approach: blood lead levels (clinical physiology), qRT-PCR (molecular genetics), brain and primary neuronal culture immunology (immunohistochemical and cellular approaches), physiological cellular components (synaptosomes and protein expression) and finally through learning and memory assessment with GABA mimetic drug manipulations in the intact animal (behavioral pharmacology). The influence of a 956ppm Pb2+ gestational diet (i.e. from birth to sacrifice) resulted in pup mean blood lead levels (BLLs measured in ìg/dL) (Range 28-47) and Dams (Range 33-51) respectively. In contrast, control pups and dams were Pb2+ negative. These ages were selected to determine neurodevelopmental trajectories of the GABA-shift from excitation-to-inhibition postnatally in our model. qRT-PCR studies evinced a delay in mRNA expression regulating GAD 80, 65, CACAN â3, GABAAR and were differentially regulated cortex and hippocampus as a function of age in response to Pb2+. Brain slice immunohistochemistry revealed an early shift of KCC2 expression in both cortex and hippocampus. Notably, these alterations were differentially regulated by age, brain region and subcellular circuitry within structures (i.e. DG vs. CA3). Neuronal cultures revealed that in response to Pb2+ at low micro molar concentrations induced VSCC-â3 nuclear translocation and GABAAR upregulation. KCC2 expression was inhibiting in cultures by Pb2+. Synaptosomal effects of Pb2+ revealed altered glutamate accumulation and handling with increased spontaneous and decreased evoked release in significantly modulated by Pb exposure suggesting altered brain synaptogenesis. Pb2+ exposure resulted in increased binding suggesting post synaptic modification in cortex and hippocampus increasing brain excitability. Behaviorally, Pb2+ exposure resulted in increased anxiety, impulsivity, stress, and disrupted learning and memory regulated by inhibitory circuits that were recovered with taurine, a GABAAR agonist, administration. Specifically, Pb2+ disrupted contextual and auditory associative learning. Taken together, these results suggest that Pb2+ interferes with early VSCCs and GABAAR synergistic action that establishes GABAergic neural networks and in turn produces increased brain excitability and over reactivity as a consequence of reduced inhibition.