Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • Diet and feeding strategies of redbreast sunfish (Lepomis aurtitus) and bluegill sunfish (Lepomis macrochirus) in two suburban lakes.

    Author:
    Linda Lalicata
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Joseph Rachlin
    Abstract:

    This is a study of the feeding habits of two species of sunfish, Lepomis auritus (Linnaeus, 1758), redbreast sunfish, and Lepomis macrochirus Rafinesque, 1819, bluegill sunfish, co-occurring in two suburban lakes with different degrees of shoreline development. Since it has been well-documented that other animal species change their dietary habits during or just prior to breeding season, it seemed sensible to determine if sunfish also exhibited this behavior. The two study lakes are close in proximity in Putnam County, New York. Lake Mahopac is a more urbanized setting, close to road traffic, surrounded by homes, and has little to no vegetation due to the introduction of grass carp. Long Pond is in a more pristine setting with one side being entirely wooded. It is not close to any main roads and there are few houses on the perimeter. The vegetation is for the most part undisturbed except for a small amount removed from its beach areas. Despite the lack of vegetation, Lake Mahopac still has as much species diversity as Long Pond. Unfortunately the bluegill population in Lake Mahopac has suffered from the lack of weed beds, which are necessary for successful breeding, which has resulted in a steady decline in numbers. The redbreast sunfish population in Long Pond is very small, most likely due to the fact that redbreast sunfish prefer moving water and Long Pond is relatively stagnant. Breeding season usually starts in May and ends in August; the exact time changes from year to year based upon weather conditions. Female bluegills from Lake Mahopac exhibited a dietary shift in which they fed opportunistically during the pre-breeding season (when water temperature is below 20° C), but shifted to that of a specialist during the breeding period (when water temperature is between 20° C to 28°C) and post-breeding (when water temperature once again begins to cool). When water temperature falls below 20° C in the fall, sunfish move to deeper waters until the following spring when the water once again warms up and they move to the shoreline to breed. There is some dietary overlap between the species, especially between females during pre-breeding, as well as between male and female redbreast sunfish from Lake Mahopac and male and female bluegills from Long Pond, indicating that if food sources become scarce they could develop both interspecific competition between females and intraspecific competition between the sexes in each lake.

  • IMPACT OF ODORS ON PATERNAL RESPONSIVENESS AND ASSOCIATED NEURONAL ACTIVITY IN "EXPECTANT" MALE PRAIRIE VOLES (Microtus ochrogaster),

    Author:
    Damaris-Lois Lang
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Dr. Maryam Bamshad-Alavi
    Abstract:

    Prairie voles (Microtus ochrogaster) are unusual mammals because they are socially monogamous. The breeding pairs form pair bonds and jointly care for offspring. Although the duration and intensity of parental behavior in male prairie voles is similar to that observed in females, there are sex differences in the onset and pattern of infant caring in this species. The factors that contribute to sex differences in parental behavior of prairie voles are unknown. As males and females show all components of active and inactive parental behaviors, it is possible that sensory inputs from infants arouse a different pattern of parental care in each sex. Males and females may also differ in the degree of attentiveness to infant sensory cues and to other environmental stimuli. Furthermore, they may focus their attention on different aspects of infant cues or perceive the same cues differently. I conducted three experiments to test these hypotheses. In the first experiment, I tested the attentiveness and sensitivity of male and female prairie voles towards infant-related odors across the reproductive period. Males and females showed increased attentiveness to infant-related odors at different times during the reproductive period. In the second experiment, I examined the impact of female sensory cues on male responsiveness towards infant odors. The data suggest that male's exposure to the female's tactile and distal cues during the gestation period elicited indirect paternal behavior in presence of infant odors. However, infant odors alone were insufficient to stimulate direct paternal responsiveness in these males. In the third experiment, I studied the neuronal activity of brain areas that could be involved in the enhanced indirect paternal behavior that was observed in males housed with their mate through mid gestation. In response to infant-related odors, males that had stayed with their mate had higher neuronal activity in the ventral tegmental area (VTA) compared to males that had stayed with their same-sex sibling. Together, these studies indicate that female sensory cues in prairie voles play an important role in enhancing indirect paternal care by increasing the male's attentiveness to odors and activating neurons in the VTA region of his brain.

  • Lichen Taxonomy for the 21st Century: A Revision of the Genus Lepraria s.l. in North America north of Mexico

    Author:
    James Lendemer
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    William Buck
    Abstract:

    The results of a series of studies of lichens are presented. These studies are hoped to codify a forward for taxonomic progress in the group. Chapter one presents a standardized morphological terminology and descriptive scheme for the sterile crustose genus Lepraria. Chapters two through seven present a series of studies where molecular phylogenetic analyses of nrITS sequence were used to resolve species boundaries in Cladonia (III), Lepraria (IV-VII), and Punctelia (II). Chapter eight reveals not all sterile crustose lichens resemble their congeners. Chapter nine presents a study in the use of molecular data to place an unknown sterile crustose lichen in higher level classification of fungi. Chapter ten uses that method to revise the circumscriptions of Lepraria and the sterile fruticose genus Leprocaulon. Finally, chapter eleven comprises a taxonomic revision of the crustose species of Lepraria s. str. that occur in North America north of Mexico.

  • Regulation of anti-dsDNA B-cells in mice transgenic for the heavy and light chains of an Anti-dsDNA antibody

    Author:
    Rita Lewis
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Linda Spatz
    Abstract:

    Regulation of anti-dsDNA B-cells in mice transgenic for the heavy and light chains of an Anti-dsDNA antibody By Rita H. Lewis Advisor: Professor Linda A. Spatz The diversity of the B-cell repertoire is important for the development of antibodies to a multitude of pathogens. However, in the process of generating antibody diversity, B-cells arise that produce antibodies to self-antigens. These autoreactive B-cells must be kept in check lest they secrete autoantibodies that can induce autoimmune disease. There are several mechanisms inherent in the immune system for regulating autoreactive B-cells. I have been using a transgenic mouse model, in which mice were made transgenic for the R4A IgM heavy and Vê1 light chain genes of an anti-double stranded DNA (anti-dsDNA) antibody, to study the regulation of anti-dsDNA B cells. Anti-dsDNA antibodies are the hallmark of the autoimmune disease Systemic Lupus Erythematosus (SLE). I observed that the transgenic anti-dsDNA B cells are targeted to anergy in the R4A-Cì/Vê1 mice as evidenced by arrested development, receptor down modulation, and functional unresponsiveness and reduced calcium flux in response to B-cell receptor stimulation. I also observed a relatively high frequency of transgenic B cells in the T1 but not the T2 or mature stages of development. In addition, transgenic T1 B cells were observed to display features of anergy suggesting that the T1 stage may be a regulatory checkpoint where anti-dsDNA B cells are anergized and subsequently eliminated. Interestingly, transgenic B-cells that were able to transition to the T2 and T3 stages of development tended to co-express an endogenous heavy chain while the majority of mature B cells in these mice expressed the endogenous heavy chain only. Surprisingly, however, B-cells expressing only the endogenous heavy chain on their membrane were also observed to express transgenic heavy chain transcripts. These results have led me to propose a model whereby autoreactive B cells can escape a regulatory checkpoint if they express more than one heavy chain. These dual receptor expressing B-cells may have diminished autoreactivity if the level of membrane expression of the transgenic heavy chain is low relative to the level of expression of the endogenous heavy chain. Subsequent down-regulation of the transgenic heavy chain as a B-cell matures in the periphery may be a novel mechanism for averting autoreactivity.

  • Hyper-activated protein kinase C mediates the reduced AMPA receptor surface expression in prenatal cocaine exposed brains: the role for diacylglycerol, diacylglycerol kinase, and 3-phosphoinositide-dependent kinases.

    Author:
    Jingjing Liu
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    hoau-yan wang
    Abstract:

    Abstract Hyper-activated protein kinase C mediates the reduced AMPA receptor surface expression in prenatal cocaine exposed brains: the role for diacylglycerol, diacylglycerol kinase, and 3-phosphoinositide-dependent kinases. By Jingjing Liu Advisor: Professor Hoau-Yan Wang Prenatal cocaine exposure induced neurobehavioral and synaptic changes are in part mediated by the defected alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-type glutamatergic receptor (AMPAR) neurotransmission. This abnormality of AMPAR system is related to reduced AMPA-GluR2/3 synaptic targeting, which is resulting from sustained phosphorylation of glutamate receptor-interacting protein (GRIP) by hyper-activated protein kinase C (PKC) (Bakshi et al., 2009). The underlying molecular mechanism responsible for PKC hyper-activation, however, remains obscure. Blockade of PKC and PKC/M by their specific pseudosubstrate inhibitors restores AMPAR synaptic targeting, demonstrating that PKC is essential in producing AMPAR abnormalities in prenatal cocaine exposed animal brains. The enhanced PKC activation by prenatal cocaine exposure correlates with an elevated 3-phosphoinositide-dependent protein kinase-1 (PDK1) level, and a persistent increase of synaptic membranous diacylglycerol (DAG) level resulting from down-regulated GRIP-associated DAG kinase (DGKγ and DGKζ) subtypes. Altogether, these data provide the molecular underpinning for persistent PKC activation in prenatal cocaine-exposed brain and suggest that suppression of PKCγ and PKC/PKMζ can restore GluR2/3 synaptic targeting and AMPAR function. Importantly, the data derived from this study may provide a novel strategy to treat neurobehavioral abnormalities resulting from prenatal cocaine exposure.

  • Characterization of the Sinorhizobium meliloti ExoR protein

    Author:
    Haiyang Lu
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Hai-Ping Cheng
    Abstract:

    The soil bacterium Sinorhizobium meliloti is capable of establishing a symbiotic relationship with its leguminous plant host alfalfa by forming nitrogen-fixing root nodules through a series of signal exchanges and structural changes. The presence of a potential bacterial signal molecule, succinoglycan, is required for the invasion step of this symbiosis. The production of succinoglycan, which is inversely coupled with the production of flagella, is tightly regulated by the S. meliloti ExoR protein and the ExoS/ChvI two-component regulatory system. To better understand the regulatory function of ExoR and its relationship with the ExoS/ChvI system, I have carried out extensive genetic and biochemical analyses of ExoR and ExoS proteins. I found that ExoR is a periplasmic protein and it functions only in the periplasm. Interestingly, the C-terminal 20 amino acids appear not to be essential for the regulatory function of ExoR. Most importantly, the ExoR protein is digested in the periplasm, which appears to be the molecular mechanism regulating the amount of functional ExoR protein in the periplasm. The genetic analysis of my collection of exoR, exoS, and chvI mutants suggests that ExoR functions upstream of the ExoS/ChvI two-component signal transduction pathway. This conclusion was further supported by the analysis of the exoR expression in different genetic backgrounds, which suggests the ExoR-ExoS-ChvI pathway is feedback regulated by ExoR. The combination of biochemical and genetic analyses suggest that ExoR functions in the periplasm through interaction with the ExoS sensing domain to keep ExoS in the off state. The proteolysis of ExoR would reduce the amount of functional ExoR and lead to the activation of ExoS and the expression of the genes regulated by the pathway. With the continuous discovery of ExoR/ExoS/ChvI homologous systems in a wide range of bacteria, my findings will contribute to a better understanding of the S. meliloti-alfalfa symbiosis and the pathogenicity of some bacterial plant and animal pathogens.

  • Antimalarial Benzophenones and Xanthones from Garcinia species

    Author:
    James Lyles
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Edward Kennelly
    Abstract:

    Garicina, a genus in the Clusiaceae, is a source of antiparasitic and antimalarial phenolic secondary metabolites, including benzophenones and xanthones. The methanolic extracts of G. livingstonei, G. mangostana, G. spicata, and G. xanthochymus were tested in vitro for antiplasmodial activity against the P. falciparum clone D6. The crude methanolic G. mangostana extract inhibited the clone by 89%, while the G. xanthochymus extract inhibited it by 24%. Neither of the extracts showed any cytotoxicity toward Vero cells. Hexanes, EtOAc, and n-BuOH partitions of a G. xanthochymus seed extract were also screened against the P. falciparum clone D6, the hexanes partition inhibited the clone by 58%, the EtOAc and n-BuOH partitions showed no inhibitory activity. Additionally, compounds identified from Garcinia species were screened in the plasmodial lactase dehydrogenase (pLDH) activity assay. The compounds tested were: aristophenone A (1), cycloxanthochymol (2), gambogenone (3), guttiferone A (4), guttiferone E (5), guttiferone H (6), isoxanthochymol (7), xantochymol (8), xanthone (9), mangiferin (10), alloathyriol (11), alpha-mangostin (12), beta-mangostin (13), 3-isomangostin (14), 8-desoxygartanin (15), 4-methoxyxanthone (16), 1,5,6-trihydroxyxanthone (17), and 32-hydroxy-ent-guttiferone M (18). Only compounds 5, 6, 7, 12, 13, and 14 showed antiplasmodial activity. The antiplasmodial activities of compounds 5, 6, and 14 have not been previously reported. This is the first report of 7, 12, and 13 having antiplasmodial activity against the chloroquine-sensitive P. falciparum clone D6 and chloroquine-resistant clone W2. For the benzophenones 8 and 2 the absence of a terminal methylene on the C-8 side chain (cf. 5 and 7) correlates with antiplasmodial activity. Compound 6 with a terminal methylene on C-30 and a cyclohexane from C-7 to C-8 is antiplasmodial. It was concluded that, for benzophenones neither the C-5 nor the C-14 side groups affect antiplasmodial activity. The substitution pattern of both the A and B rings of the xanthones was shown to be important in determining the extent of antiplasmodial activity. An isoprenyl chain was necessary on C-8 for antiplasmodial activity (cf. 12 and 14). The results indicate that the antiplasmodial activity is determined by factors other than the hydroxylation of C-4 and C-5 alone as the current structure activity studies indicate.

  • Habitat association and spatial distribution of Procellariiform seabirds along the continental shelf of the northeast of the United States and southeastern Canada: Relationships to prey and other top predators

    Author:
    Marie Martin
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Richard Veit
    Abstract:

    In the first chapter, I compare habitat association among seven species within the order of Procellariiform seabirds that includes shearwaters, storm-petrels and northern fulmars (Fulmarus glacialis) along the northeastern continental shelf of the United States and southeastern Canada (Northwest Atlantic). Environmental factors such as bathymetry, sea-surface temperature (SST), chlorophyll concentration, and frontal features affected seabird densities and influenced their distribution. My model suggested that some species could be influenced by changes to large-scale hydrographic features and that all species will not respond equally to potential climatic fluctuations. In the second chapter, I focus on the northeast Georges Bank and Jeffreys Ledge regions of the Gulf of Maine, recording the presence of marine predators during four hydroacoustic surveys. The primary objective of these surveys was to make annual assessments of the pre-spawning stock of Atlantic herring (Clupea harengus). I explain the interannual variability of top predators (seabirds, dolphin, whale) using a general additive model that included environmental parameters and fish acoustic index to understand the possible reasons of this variability, including: 1) the effect of environmental predictors on top predators and prey; 2) piscivorous marine predator abundance correlated to fish acoustic biomass index data; and 3) the effect of fishing vessel density effect on marine predators. All predators and Atlantic herring were affected by oceanographic variables; northern gannet (Sula bassana) by fish density, as well. There were also spatial overlap between fishing vessels, humpback whales (Megaptera novaeangliae), great shearwaters (Puffinus gravis) and herring gulls (Larus argentatus). This study shows the importance of accounting for multiple environmental parameters in order to understand the variability of marine predators abundance in highly productive areas such as Georges Bank, in addition to assess spatiotemporal overlap between aggregated predator and prey for improving fisheries management. Finally, in the third chapter, I examine the foraging associations between Procellariiform seabirds and one species of Pelecaniform (northern gannet), dolphins, whales, and two species of tuna along the continental shelf. The general linear model results suggested seasonality in aggregation types. Great shearwater density increased with humpback and fin whales (Balaenoptera physalus) in the summer, and shifted to common dolphin (Delphinus delphis) in the fall.

  • Genomic analyses reveal putatively pathogenic genes and functional elements in Borrelia burgdorferi, the Lyme disease bacterium

    Author:
    Che Martin
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Weigang Qiu
    Abstract:

    B. burgdorferi s.l. (B. burgdorferi sensu lato) represents a Gram-negative bacterial species complex that includes causative agents of Lyme disease. As an obligate parasite, B. burgdorferi`s persistence in nature depends on its innate ability to exist and survive in two distinct biological environments, the hard-bodied tick (vector) and small vertebrates (hosts), as it progresses through different stages of its enzootic cycle. To accomplish this feat, B. burgdorferi heavily depends on its ability to tightly regulate differentially expressed host- and vector-specific genes. However, very little is known about the genes and regulatory elements contributing to the pathogenicity of this increasingly prevalent pathogen. This is primarily due to the fact that B. burgdorferi is not a model organism and is difficult to culture and transform. Additionally, we were previously limited in our ability to do comparative genomic studies in this organism due to the unavailability of whole-genome sequences. The recent release of whole-genome sequences from 22 strains spanning 8 different genospecies of B. burgdorferi has since made it possible to conduct a comprehensive genome study in this organism. Here, we employ phylogenomics analyses (analysis of the genomes of a group of closely related species) on the core genome of B. burgdorferi in order to identify putative genes and functional elements that may contribute to the pathogenicity of this organism. We conducted three main analyses: i) test of positive natural selection within the coding regions of the core genome replicons, ii) test of evolutionary constraints within the non-coding regions of cp26 and lp54, and iii) structural and phylogenetic comparison of OspA and OspB (Outer Surface Protein A and B), two paralogous virulence-associated lipoproteins. Consequently, we identified three genes putatively involved in adaptive host immunity, fifteen genes putatively involved in adaptive divergence, two new genes putatively under direct transcription RpoS (an alternative regulatory subunit of RNA polymerase), a number of putative cis and trans-acting regulatory elements, and fourteen fixed differences between OspA and OspB concentrated in the region proximal to the C-terminus barrel domain and the N-terminus globular domain. These findings highlight a number of coding and non-coding sequences that may contribute to the virulence of Borrelia burgdorferi in humans. These findings provide a basis for future experimental studies towards the discovery of therapeutic, diagnostic, and preventive approaches to Lyme disease.

  • The Role of Soluble Adenylyl Cyclase in the BDNF-Dependent Block of MAG/Myelin-Mediated Inhibition

    Author:
    Jennifer Martinez
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Marie Filbin
    Abstract:

    In the adult mammalian central nervous system axons do not spontaneously regenerate following injury. This lack of axonal regeneration is partly due to the presence of inhibitory proteins, such as myelin-associated glycoprotein (MAG). Previously, we showed that elevating cyclic AMP (cAMP) by pretreating (priming) neurons with neurotrophins, such as brain-derived neurotrophic factor (BDNF), is sufficient to overcome the block of axonal outgrowth by MAG. Additionally, we demonstrated this BDNF-mediated effect to be PKA-, ERK-, calcium- and CREB-dependent. However, increasing cAMP levels in response to BDNF could be dependent on several factors. A balance between the production of cAMP by adenylyl cyclases and its degradation by PDEs will determine intracellular cAMP levels. Given that the source of the cAMP produced in response to BDNF is unknown, we sought to investigate which adenylyl cyclase is activated, transmembrane adenylyl cyclase (tmAC) or soluble adenylyl cyclase (sAC). tmACs and sAC differ in their spatial localization within the cell, structure and regulation. Our hypothesis is that the rise in cAMP in response to BDNF priming is partially dependent on sAC activation. In this study, we have detected an isoform of sAC, somatic sAC, expressed in various postnatal rat primary neurons and demonstrated that specifically blocking sAC with the pharmacological inhibitors, KH7 and OH-E or by knocking down sAC expression with siRNA, abolishes the ability of BDNF to overcome inhibition by MAG. Additionally, infection of primary neurons with a lentivirus that expresses sAC is sufficient to overcome the block of axonal growth by MAG and myelin in vitro and promotes optic nerve regeneration in vivo. As previously mentioned, priming with BDNF leads to ERK activation, which results in overcoming MAG-induced inhibition of neurite growth. We found that blocking sAC with pharmacological inhibitors blocked the BDNF-dependent phosphorylation of ERK whereas blocking tmAC had no effect on ERK activation by BDNF. Lastly, we sought to determine if alternative modes of sAC regulation exist, such as interactions with TrkB. Our data demonstrated that sAC does not associate with inactive or active TrkB receptors, yet does not rule out that other potential modes of regulation may exist. Taken together, our data suggest that sAC plays an integral role in BDNF signaling to overcome inhibition of axonal growth by MAG.