STUDENT ABSTRACTS

This thesis reports on the results from the summer 2008 and 2009 total solar eclipse expeditions as well as the data received during the stellar occultation event of KBO 55636 (2002 TX300) during October 2009. I discuss the basics of total solar eclipses and occultations and highlight some of the past observations made during these astronomical events. While the alignment of the data from the August 1, 2008, eclipse is incomplete, we were able to align the data to within a few pixels and run FFT analysis on the green line data. This thesis explores many ways to approach the alignment procedure, some with more success than others. For the occultation data, we measured the intensity of the occulted star and compared it to the surrounding stars in the field. While we did not observe an occultation, our location on Oahu, Hawaii, became an important limit to the size and shape of the Kuiper Belt Object. Using data from two successful locations, our colleagues were able to place constraints of the object including size, shape and albedo.

In this thesis we present chemical abundances for 16 PNe in the halo and thick disk of Andromeda Galaxy (M31). We find that our abundances exhibit strong Ne/H v. O/H and N/O v. N/H correlations, in agreement with relationships found for PNe in the Milky Way (MW). Derived metallicities for our sample are higher than metallicities in RGB stars. Because our PNe progenitors are from the same stellar population as RGB stars in M31, our data supports the claim that oxygen may not be a reliable indicator of overall metallicity.

BIOLOGY

Vincristine (VCR) is a commonly employed chemotherapeutic agent for the treatment of acute lymphoblastic leukemia, the most frequent childhood malignancy. Despite its clinical efficacy for treating this disease, VCR induces high-incidence, rapid onset peripheral neuropathy (VCR-PN), which manifests itself as high-degree symmetric distal muscle paresis (foot and wrist drop). Our understanding of VCR-PN pathogenesis, however, remains fragmentary. Here we deploy a zebrafish model system to characterize the behavioral and cellular bases of VCR-PN. We utilize high-speed video recording and kinematic analysis to demonstrate that VCR potently impairs touch responsiveness and coordination of touch-evoked swimming in a dose-dependent manner without causing gross morphological defects. This uncoordinated motor behavior is ostensibly due, at least in part, to VCR-induced degeneration and impairment of motor axon arbor branching and outgrowth. Furthermore, we are the first to describe the characterization of VCR-PN in motor neurons using a transgenic zebrafish model of axonal Charcot-Marie-Tooth Disease Type 2F (CMT2F). While human CMT patients in some cases experience exacerbated VCR-PN, CMT2F transgenic zebrafish and their otherwise-wildtype siblings were equally sensitive to VCR-PN.

Epilepsy and neurological disorders have long been associated with severe seizure attacks. To date, the mechanism behind having a sensitivity to seizures is poorly understood. However, evidence suggests that metabolic pathways such as the insulin pathway may be involved in causing seizures. In Drosophila, studies have identified the slamdance (sda) allele sda^iso7.8, which exhibits a seizure-like phenotype. We have previously suggested that sda^iso7.8 might be regulated by the insulin pathway because of its interaction with the transcription factor dfoxo. Despite this, it is still unknown whether other insulin pathway effectors associated with dfoxo can modulate seizure sensitivity. Here we identify some upstream effectors of dfoxo in the insulin pathway that are able to modulate the sda^iso7.8 phenotype. We misexpressed dfoxo in muscle, nervous system and fat body in both adults and larvae. Results show that dfoxo only affects bang sensitivity in the adult nervous system. We also found that PI3k, an upstream regulator of dfoxo and SK6, a member of the TOR pathway, modulates bang sensitivity in sda^iso7.8 heterozygotes. Our results suggest that both the insulin and TOR pathways are able to affect the presence of a seizure. We anticipate that identifying other genes that interact with sda^iso7.8could act as a model to study the role of the insulin pathway in regulating seizure disorders.

I constructed and analyzed a series of population models for the Pseudacris maculata populations of Isle Royale National Park. Using censuses of tadpole populations from 1982 through 2009 and repeated censuses of Edwards Island from 2009 I performed simulations of the models I had constructed, estimated the observational error in the census data and performed fitting of model parameters accounting for error. Modeling of population dynamics within the study area produced a variety of models allowing for different handlings of spatial and age structure. A model of the study system incorporating a density dependent dispersal function was established for the first time.

This study addresses ecological processes that allow closely related species to maintain unique genetic identities. The New England aster and goldenrod (Asteraceae) biodiversity hotspot includes Berkshire County, Massachusetts, so Williamstown is an ideal location to investigate postzygotic mechanisms of reproductive isolation among sympatric angiosperms. Field data from fall 2009 indicate that species uniqueness is a function of three factors. First, spatial segregation along broad and fine scale gradients can maintain species differences. We show that Eurybia divaricata (typically below 1,700 ft. elevation and Oclemena acuminata (typically above 1,700 ft. elevation) separate on an elevational gradient on Mt. Greylock. On a finer scale, Symphyotrichum spp. and Solidago spp. separate by microhabitat, with Symphyotrichum puniceum and S. lanceolatum preferring moist soil and Solidago gigantea and S. canadensis preferring dry habitats. Second, different blooming times can maintain separation by reducing the likelihood of cross-pollination and hybridization. We show that the goldenrods (Solidago spp. and Euthamnia graminifolia) bloom earlier than asters (Symphyotrichum spp. and Eurybia divaricata). Third, gene flow mediated by pollinators can maintain segregation. Individuals of four common local pollinators (Apis mellifera, Bombus impatiens, B. ternarius, and a syrphid fly) all showed complete loyalty. In 209 minutes of observations, of 73 insects, all individuals only visited one flower species. None switched between species even when multiple options were available in the same field. All three separation patterns illustrate both the phylogenetic niche conservatism concept and the niche complementarity hypothesis, with closely related plants behaving similarly and more distantly related taxa interacting strongly to occupy different ecological niches and shape the spatial and temporal structure of the fall-blooming aster and goldenrod community.

One hour after selective axotomy of the goldfish Mauthner cell axon, reactive cells respond to the proximal and distal tips of the severed axon. Their apparent attraction to injury, nuclear morphologies, and their presence in the central nervous system suggest these reactive cells to be macrophage/microglia. In the rat and leech, the attraction of microglia is dependent on the extracellular release of ATP. The present study investigated the reactive cell response to an injury of minimal damage to the Mauthner axon and an introduced ATP signal. Reactive cells associate with minimally damaged Mauthner and non-Mauthner axons in the dorsal FLM. Some of these reactive cells were confirmed to be macrophage/microglia phagocytosing myelin debris. Reactive cells also responded to localized application of ATP. Microglia were confirmed as the first responders to damage and may respond to an ATP signal in vivo in the goldfish CNS.

The plant pathogen Agrobacterium tumefaciens causes the formation of characteristic ‘crown gall’ tumors by transferring a portion of its DNA (T-DNA) into the host cell. This unique cross-kingdom DNA transfer event is controlled by a set of virulence (vir) genes located on the tumor-inducing plasmid (pTi), which is required for infection. These vir genes are expressed in the presence of acetosyringone (AS) under vir-inducing conditions. During infection, the T-DNA is transferred through the prototypical type IV secretion system (T4SS) encoded by the virB operon, which is controlled by an AS-dependent promoter in front of virB1. In addition to this promoter, the Banta Lab has discovered a novel internal promoter located between virB6 and virB7. Previous work has demonstrated that the identified sequence does function as a promoter and interestingly appears to be repressed by AS. Because of its location and constitutive relatively low activity in non-induced cells, we suggest that the internal promoter plays a role in the initial attachment process. Here we show using RT-qPCR that the internal promoter is active upon host-attachment under non-inducing conditions. We have also begun to characterize the 5’ end of the mRNA transcript emanating from the internal promoter using 5’ RACE. Our data suggest that the internal promoter allows for an extra level of control over the expression of virB genes, specifically upon host cell attachment. We propose a model in which this internal promoter drives production of a subset of VirB proteins necessary in the early stages of T4SS assembly, prior to AS-induced vir gene expression. The presence of low levels of VirB8, which has been shown to nucleate formation of a complex comprised of the core T4SS proteins and to target that complex to specific foci within the cell envelope, could thereby prime the bacteria for infection when the opportunity arises.

The genetic structure of a population reveals the interaction of forces that drive evolutionary change. In this study, I use twelve neutral microsatellite DNA markers to determine effective population size and population genetic structure in the boreal chorus frog (Pseudacris maculata) on North Government Island in Isle Royale Wilderness Park, Michigan. On North Government Island, frogs breed in small pools along the rocky shore of Lake Superior in two ecologically distinct habitats for tadpoles: pools near the forest contain odonates that prey on tadpoles, while closer to the lake there are few predators. Tadpoles show a different phenotype in the presence of predators than when they are in a predator-free environment, suggesting that selection or phenotypic plasticity is occurring in this population.

I found three important results. First, there is no genetic difference between tadpoles on the upper and lower shoreline, but clear genetic differentiation along the shoreline of the island. This indicates that gene flow along the shore is restricted, but not gene flow between microhabitats. Secondly, sibships are distributed among pools along the shoreline, suggesting that individuals move farther distances than previously shown. Finally, population allele frequencies fluctuate over time, suggesting small effective population size. Estimates using Wang’s (2009) method indicate that effective population size is low, between 42 and 56. This indicates that drift is acting upon the population so that selection must be relatively strong to have a significant effect. Movement between habitats indicates that phenotype differences between habitats are likely to be due to a plastic response in the tadpoles, not local adaptation.

Carrier zebrafish harboring the S135F mutation were found to have developmental phenotypes identical to their non-carrier siblings. Furthermore, application of stress using heat shock or pharmacological inhibition of the ubiquitin-proteasome degradation pathway did not reveal the carriers to be preferentially susceptible to developmental defects. We thus establish that the effects of the CMT2F causing S135F mutation is manifested not during development but through processes arising later in life.

During the course of our pharmacological inhibition of the proteasome, we discovered that one compound, bortezomib, causes significant impairment of zebrafish motoneurons by causing reduced axonal branching and swimming defects. Bortezomib-induced peripheral neuropathy (BiPN) is a significant side effect of bortezomib chemotherapy for multiple myeloma. Our work therefore establishes the zebrafish as a useful model to study BiPN and lays down the groundwork for future studies.

Small heat shock proteins (sHSPs) are a family of molecular chaperones characterized by a conserved α-crystallin protein-binding domain. sHSPs bind to proteins to prevent their aggregation and bind to cytoskeletal elements to influence cytoskeletal dynamics. Many are upregulated upon heat shock and other stresses, and are typically studied for their role in the heat shock response of mature organisms. Two non-heat-shock regulated small heat shock proteins, hspb7 and hspb12, are expressed specifically in the developing vertebrate heart. We have carried out loss-of-function experiments in zebrafish to examine a developmental role for these proteins. hspb7 is present in all vertebrates, while hspb12 is found only in fish and birds. These two proteins are closely related; however, a functional relationship between them has not been investigated, and the complete coding sequence of hspb12 has not been established.

Beginning at 12 somites, hspb7 has bilateral expression domains in the lateral plate mesoderm (LPM), overlapping with the heart precursor fields, before moving to the heart and somites. We found that morpholino (MO) knockdown of hspb7 causes concordant randomization of internal situs, suggesting that this gene has a role in establishing global left-right asymmetry. This phenotype is a result of abnormal, bilateral expression of southpaw, a zebrafish nodal gene and left-side determining factor. This effect, however, is not mediated by gross changes in Kupffer’s vesicle or its cilia, the developmental organ necessary for establishing left-right asymmetry. Normally, hspb7 most likely contributes to right-sided repression of southpaw.

We verified the full coding sequence of hspb12 and found that it does not have an alternative translational start site. hspb12 is expressed in zebrafish heart fields beginning at 17-18 somites. MO knockdown of hspb12 causes a partial randomization of heart situs, and an increase in non-jogging, midline hearts. Knockdown of hspb12 has little effect on southpaw expression and results in heterotaxy rather than concordant asymmetry defects. This gene is most likely necessary for downstream readouts of laterality signals. Double-knockdowns of hspb7 and hspb12 suggest that these two genes work together to affect left-right asymmetry. These phenotypes represent the first known developmental patterning roles for small heat shock proteins.

The herbaceous perennials Clintonia borealis (Liliaceae) and Linnaea borealis (Caprifoliaceae) often co-occur in northern boreal forest ecosystems. C. borealis is a monocot; L. borealis is a eudicot. Although the two species are distantly related, there is potential for interspecies interactions: the two plants grow in similar habitats, reproduce at similar times, and their similar flower structure (pendant bell-shaped flowers) may attract similar insect visitors.

Flowers of both Clintonia borealis and Linnaea borealis are visited by a similar subset of insect species (including bumblebees and larger syrphids, like Temnostoma venustum) suggesting that competition for pollinators may play a role in flowering times. To investigate the complex role of insects in mediating and influencing gene flow, we observed the suite of insect visitors that visit each plant species and two other co-blooming species, Cornus canadensis and Aralia nudicaulis, which have clusters of small white flowers. For all visitors we recorded their foraging behavior, and scored their pollen loads by counting and identifying the pollen grains the insects carried to the species level.

We found that the behavior of insects visiting each species differed markedly. Pollen loads of insect visitors to Clintonia borealis consistently carried a wider variety of pollen from different species (up to 7 different species) whereas the pollen loads from insect visitors to Linnaea borealis carried predominately (and in some cases, exclusively) L. borealis pollen. The patterns held even for the same species of insects, indicating individual insect behavior varies within a species—with high loyalty displayed when visiting L. borealis and low loyalty when visiting C. borealis. The species of insects visiting Linnaea borealis and Clintonia borealis showed little overlap with species visiting Aralia nudicaulis and Cornus canadensis. Only Bombus (bumblebee) overlapped as a visitor on all four plants: C. borealis, L. borealis, A. nudicaulis and C. canadensis.

Birdsong is currently the best animal model system for human speech. Previous research explored associations between brain space for song and salient features of the song, and in multiple songbird species showed that the number of syllables a bird sings is positively associated with the size of one song control nucleus, HVC. However, electrophysiological and lesion studies suggested that HVC plays a larger role than simply encoding distinct syllables These studies linked HVC to the syntax, or ordering of the syllables. HVC size has not previously been compared to measures of sequence complexity or syllable structure, and the sizes of other nuclei involved in song production, Uva, RA, and LMAN, were not reliably associated with any song measure previously assessed. This study examines measures of syntax, syllable structure, and syllable repertoire size, and compares these to the carefully measured volumes of song control nuclei in Bengalese and zebra finches, two related species with marked differences in syntax complexity. Performing multiple regression modeling for nucleus size revealed that larger HVC volume is predicted by a larger syllable repertoire size, greater variability in syllable structure, and greater variability in the possible syllables ending a song bout. Uva volume is predicted by a higher total number of syllables, fewer different syllables, and greater consistency in acoustic structure across renditions of the same syllable. There is also a significant positive association between Uva volume and a measure of repeats in Bengalese finches. Larger LMAN volume is predicted by lower entropy when syllable-to-stop transitions were excluded, lower syllable-to-stop entropy, and greater inter-syllable similarity. These models are discussed in the context of current research in the field.

In Arabidopsis thaliana, three isoenzymes of inositolphosphorylceramide synthase (IPCS) have been found to mediate the ceramide to inositolphosphorylceramide (IPC) reaction. The actions of these enzymes are necessary for the plants to survive, though it is not exactly clear why this is the case. We examined the possibility that the products of this ceramide to IPC reaction play a crucial role in the unidirectional transport of the essential plant hormone auxin. Auxin is transported down the plant via influx and efflux receptors. We believed that the localization of some of these receptors might be partially dependent upon proper amounts of IPC and glycolsylated IPC (GIPC) in plasma membranes. In our attempts to test this hypothesis, we found that the RNAi lines used by Nina Ivanova ’09 were no longer knocked down, necessitating our usage of a different line of plants with decreased IPCS activity as a result of T-DNA insertion mutagenesis. We show that the S5-ERH-1 line has decreased IPCS RNA, decreased activity and differing lipid membrane composition. However, we did not find evidence of a change in localization of the PIN-1 receptor in 2-day-old plants. These findings, though, do not rule out the possibility that other efflux receptors might be influenced even in the ERH-1 lines, or that delocalization may occur later in plant development.

The tadpoles of the boreal chorus frog (Pseudacris maculata) live in the many small pools scattered across the rocky shoreline of Isle Royale, Michigan. Within this subdivided environment, survival varies by pool. Observation of tadpole sizes and pool occupancy shows that tadpoles of similar size often occupy groups of nearby pools along the shoreline, implying that tadpoles within these clustered pools may be members of the same full-sibling family. In this study, I use highly polymorphic microsatellite markers to reconstruct full and half-sibling families within North Government Island and determine if observed geographical clusters of similarly sized tadpoles are sibships.

The dispersal patterns of full and half-sibling broods can be used to reconstruct the movement and breeding patterns of adult frogs. Adults frequently move between pools during amplexus, and this movement mitigates the potential effects of selection. Distribution of offspring among pools decreases uncertainty of reproductive success and variation in reproductive success, thus decreasing the impact of selection by pool on genetic diversity and effective population size.

High-speed movements in plants represent a diverse set of mechanisms, which can aid in the dispersal of genetic material. We examined the biomechanics and ecological significance of high-speed movements in three different species: the exploding fruits of the pale touch-me-not, Impatiens pallida (Balsaminaceae), the individually propelled seeds of sorrel, Oxalis spp. (Oxalidaceae), and the exploding flower of alfalfa Medicago sativa (Fabaceae). We compared the biophysics of these plants in the framework of Skotheim and Mahadevan (2005), determining that I. pallida uses an explosive fracture dominated mechanism while Oxalis and M. sativa employ snap-buckling mechanisms, all of which use elastic instabilities (not just swelling) to achieve their movements. Analysis of high speed video shows that I. pallida fruits rip from the top down to ballistically propel seeds at mean velocities of 3.35 m/s, dispersing their seeds both close and far to maximize offspring success by due to their life history as annual plants-- near seeds recolonize the parental site and far seeds colonize new areas. Histological studies of I. pallida, show lignin in the outer cells, but not in the inner suggesting lignin may play a role in the curling pattern. The outer and inner cells aligned at 90º from each other suggesting the possibility of A-B layer composition in controlling the curling of capsule segments. Individual Oxalis seeds are propelled at velocities of 8.67 m/s by their fleshy arils flipping inside out in 3.93 ms to disperse seeds 360º around the capsule. The seeds appear to achieve high projection angles by using interlocking grooves in the seed and aril as directional guides. M. sativa stamens and carpels snap up in 3.73 ms at speeds of 0.67 m/s via the opening of the keel enclosing them. This may enhance pollination by biotic vectors by allowing more precise pollen placement, but because the pollen is projected up to 24.9 cm, it may allow for anemophily as a back-up mechanism. The different biomechanics and functional aspects of these motions demonstrate the diversity of high-speed movements in the plant kingdom.

Agrobacterium tumefaciens causes crown gall disease, in which uncontrolled cell division leads to tumor formation, on a wide range of host plants. The bacterially derived T-DNA, which is stably incorporated into the host genome, encodes enzymes involved in the synthesis of plant growth hormones and nutritional resources for the bacterium. The transfer of T-DNA and several bacterial proteins contributing to virulence is mediated by the bacterial VirB Type IV Secretion System (T4SS) encoded by the virB operon. The two-component system VirA/VirG is responsible for vir gene induction upon perception of signals characteristic of a susceptible host plant. A second secretion system, the Type VI secretion system (T6SS), also contributes to virulence in A. tumefaciens, as the deletion of the A. tumefaciens imp genes, which encode a functional T6SS, results in attenuated virulence on tobacco and Arabidopsis. We hypothesized that this decrease in virulence may be due to the inability of the mutant to secrete, via the T6SS, effectors that are necessary for dampening host defense responses. To test this hypothesis, we monitored the gene expression of PR defense genes, the oncogene ipt, and virB4, using RT-qPCR on Arabidopsis stems or roots co-cultivated with wild-type or mutant bacterial strains. We found that in stems inoculated with bacteria expressing a constitutively active VirA, ipt levels were similar to those in stems infected with the ∆T6SS mutant. The failure of enhanced vir gene expression to restore normal transformation capacity to the ∆T6SS mutant suggests that virulence is not limited by the inability of the mutant to counter plant-induced inhibition of Vir-mediated T-DNA mobilization. Instead, we propose that the T6SS may be needed in order to secrete effectors to dampen the host silencers that typically suppress the expression of T-DNA-encoded genes after the T-DNA has been incorporated into the host genome. Taken together with data on virB gene induction and PR gene expression profiles in bacteria associated with roots, these results demonstrate the utility of a co-cultivation model to probe Agrobacterium-host signaling cross-talk.

For almost a third of epileptic patients in the United States who do not respond to anti-convulsive drugs, the ketogenic diet can be an effective, non-invasive alternative. Studies have shown that the efficacy of this a high-fat, low-carbohydrate regime may lie in its down-regulation of glucose metabolism and subsequent reduction in global ATP levels. This hypothesis prompted us to examine the roles of aerobic and anaerobic respiration pathways in modifying a seizure-like behavior in Drosophila melanogaster known as bang-sensitivity. Here we find that disruption of phosphoglycerate kinase (Pgk) in adult muscles, which impairs the glycolytic pathway locally, enhanced bang-sensitivity. In contrast, Spargel mutations, which significantly reduce mitochondrial biogenesis, suppressed bang-sensitivity. We also studied dFOXO, which is thought to be a key intermediary between the insulin pathway, a major nutrient-sensing system, and bang-sensitivity, via genes affecting mitochondrial biogenesis like Spargel. Three models have been proposed for the nature of the interactions between dFOXO and Spargel, and further work is necessary to distinguish between them.

Transfer ribonucleic acid (tRNA) is one of the primary molecules involved in the translation of DNA information into polypeptide chains. Prior to attaining its final mature and functional form, tRNA is highly processed and modified. tRNA modifications, typically single nucleotide transformations catalyzed by specific enzymes, are abundant and highly conserved across domains. However, the purpose and significance of these modifications is not well explained – particularly because many mutants lacking genes encoding tRNA modification enzymes present no observable phenotypes under normal growth conditions. Of particular interest, the transformation of uridine to pseudouridine at position 55 (Ψ55) occurs in >90% of tRNA sequences and is the most common tRNA modification across all domains of life, but this modification is still not well understood. In Saccharomyces cerevisiae, PUS4, which codes for the pseudouridine 55 synthase Pus4, has repeatedly been proven to be a nonessential gene, and no other enzyme creates the Ψ55 modification. However, select double mutant strains that lack a second modification gene in conjunction with pus4 (pus4Δtrm8/82Δ, pus4Δtrm1Δ, pus4Δtan1Δ, and pus4Δpus1Δ) lose viability at elevated temperatures (36°C). Thus the role of PUS4 and/or its catalytic product Ψ55 in S. cerevisiae may be reveled by the synthetic genetic interactions of mutants simultaneously lacking two tRNA modifications. This thesis investigates the significance of PUS4 and/or Ψ55 from a new angle; examining the potential link between the temperature-sensitive phenotype of pus4 double mutants and the cell cycle. Flow cytometery was used to study the cell cycle progression of synchronized double mutant – pus4Δtrm82Δ and pus4Δtrm1Δ – cultures when incubated at elevated temperatures (36°C) for prolonged periods of time (>2hours) as compared to wild-type and single deletion mutant cultures grown in identical conditions. Results suggest that pus4Δtmr82Δ and pus4Δtrm1Δ begin to accumulate in G1 after 2.5 hours incubation in 36°C. The accumulation of pus4Δ double mutants in G1, in contrast to the control strains’ continuous cycling, is preliminary evidence of a potential link between tRNA metabolism/modifications and the regulation of cell cycle progression in Saccharomyces cerevisiae.

Gene expression controls growth differentiation and development of an organism. From transcription to post-translational modification of a protein, any step of the gene’s expression can be regulated. Using a subtraction hybridization approach, a candidate pool of developmental regulatory genes for leeches was created based on gene expression during annelid segmentation. In this thesis I present the expression profile of ten candidate genes in Helobdella robusta and identify their homologues in other organisms, which validates the unbiased screen used to identify candidate gene products in leech development. Nine out of the ten genes were found to be Helobdella robusta homologues of dorsal, early growth response 1 (EGR1), Prospero (Pros), discs large (Dlg), pinhead1(PNH1), programmed cell death 6 (PDCD6), WNT1-inducible-signaling pathway protein 2 (WISP2), Mago nashi, GBF1, while one gene candidate remains an unknown protein with an unknown function. Expression of Hro-WISP2 suggests it might play a role in the specification of mesodermal tissue, which would parallel many of its known developmental functions in other organisms and strengthen the fact that the WNT signaling pathway has been conserved through evolution. Expression of Hro-Dorsal implies a role in M-stem cell specific formation which may be the first step in not only clarifying the developmental process of stem cells in leeches but in the long run may help identify the stem cells in other organisms as well.

The Type VI Secretion System in A. tumefaciens is encoded by the fourteen-gene imp operon. Previous work in the Banta lab revealed that mutants with a deletion of the entire imp operon exhibit elevated biofilm formation, attenuated virulence, elevated attachment to host tissue, and finally, a tendency to aggregate (Rogawski 2008) (Baccaro 2008) (Helen Cha, unpublished observations). While the mutant phenotypes of imp operon deletion mutants may be mediated by the T6SS, it is also possible that they are regulated by a separate pathway independent of the T6SS. Specifically, there is a chance that two putative T6SS regulators, impM and impN, mediate these behaviors by acting on other putative targets outside of the T6SS (Mougous et. al. 2007).

In order to test this possibility, this thesis characterizes biofilm formation, virulence, settling status, and attachment in a deletion of only the icmF homolog, impL, where all other imp operon genes are intact, including impM and impN. ImpL is crucial to the functioning of the secretion system because it is required for the secretion of Hcp, the only known substrate in. This thesis rules out the possibility that a T6SS-independent pathway controls these phenotypes by showing that the icmF mutant is a phenocopy of the imp operon deletion mutant.

Chronic 60% fructose feeding decreases the sensitivity to leptin in rats as assessed by decreases in food intake and body weight after administration of exogenous leptin. We hypothesized that a 60% fructose diet would also lead to leptin resistance in mice, as assessed by 1) a lack of response to exogenous leptin, 2) elevated circulating leptin, and 3) a lack of entry into torpor upon fasting. In experiment 1, male Hsd:NSA (CF-1) mice were fed either a 60% fructose diet or an isocaloric fructose-free diet and food intake and body weight were monitored for 3 weeks. In experiment 2, male C57Bl/6 mice were fed either a 60% fructose diet or an isocaloric fructose-free diet and food intake and body weight were monitored for 14 weeks. After respective feeding periods, mice in both experiments were injected interperitoneally with leptin (5 mg/kg) and consequent changes in food intake and body weight were monitored. High fructose feeding did not attenuate the expected hypophagic response to exogenous leptin. These observations indicate the failure of a 60% fructose diet to induce leptin resistance in a 3 week feeding period in Hsd:NSA (CF-1) mice or over a 14 week feeding period in C57Bl/6 mice.

CHEMISTRY

Though bulk heterojunction (BHJ) organic solar cells offer significant advantages over conventional photovoltaic technology, they currently suffer from low power conversion efficiency. We are working to improve the efficiency of organic solar cells by developing fluorinated poly(p-phenylenevinylene) (PPV) derivatives with the aim of influencing the morphology of the thin polymer film used in a solar cell’s active layer. Efforts have been focused on 1) synthesizing novel PPV monomers that yield soluble polymers of sufficiently high molecular weight for good film formation and 2) adjusting PPV polymerization conditions to control polymer molecular weight.

Polymer directed enzyme prodrug therapy (PDEPT), is a method of directing chemotherapy treatment towards tumors. PDEPT takes advantage of the enhanced permeability and retention effect, whereby macromolecules accumulate in cancerous tissue due to its leaky vasculature and poor lymphatic drainage systems. Thus, polymer-enzyme bioconjugates with high molecular weights (>40 kg/mol) or large diameters (>4 nm) can be selectively taken up and activate prodrugs within tumors.

Attaching polymers to proteins indubitably affects their properties; the protein is subjected to micro-environmental or even conformational changes. Polyethylene glycol (PEG) is non-toxic and increases the molecular weight and diameter of the model enzyme trypsin. Conjugation with PEG polymer lengths under 20 kDa enhances trypsin activity and preserves secondary structure under thermal stress, increasing the T_dfrom 50 to 60°C to expand the enzyme’s workable range of conditions. PEG’s ability to stabilize enzymes is also beneficial for the shelf-life of future chemotherapeutic drugs involving PDEPT.

Poly(polyethylene glycol methyl ether acrylate) (poly(PEGA)) is a PEG analog in which the ethers branch off of an acrylate backbone. An molecular weight equivalent of poly(PEGA) is shorter than PEG, but bulkier. Poly(PEGA) bioconjugation also increases the size of trypsin and confers thermal stability, but has detrimental effects on activity at lower temperatures, reducing activity 96% relative to native trypsin at room temperature. At temperatures > 40°C, poly(PEGA)-trypsin activity is revived to 80% relative to free trypsin at the same temperature. Thus, architecture and molecular weight have a significant impact on enzyme activity and stability. Currently, 10K and 20K PEG conjugates show the most promise as viable PDEPT candidates for further exploration.

The genus Streptomyces is a group of gram positive, filamentous, soil-dwelling bacteria. These bacteria are known to produce bioactive secondary metabolites, which include over two-thirds of the naturally derived antibiotics used clinically today. Essential to the biosynthesis of most antibiotics in Streptomyces are phosphophantetheinyl transferases (PPTases). They catalyze the post-translational modification of carrier protein domains with a 4’-phosphopantetheine group (P-pant) thus converting the apo-carrier protein to its activated holo-form. The Streptomyces coelicolor genome encodes three putative PPTases of which this project focuses on two, SCO5883 (RedU), and SCO6673. Previously, the RedU PPTase has been linked to the biosynthesis of undecylprodigiosin and the SCO6673 PPTase has been linked to the biosynthesis of the calcium dependent antibiotic produced by S. coelicolor. A SCO6673 knockout mutant also exhibited greater production of undecylprodigiosin, a potentially pharmaceutically useful antibiotic with immunosuppressive and anticancer activity. Manipulation of the PPTase genes is of particular interest to see if antibiotic production can be increased.

A number of PPTase overexpression strains and PPTase complementation strains were created and the effects on actinorhodin and undecylprodigiosin production were monitored with the ultimate goal of increasing undecylprodigiosin biosynthesis. Overexpression of redU in the WT background could significantly increase undecylprodigiosin production. However, overexpression of redU in the SCO6673 mutant did not increase undecylprodigiosin levels in this already hyperproducing strain. Conversely, actinorhodin production decreased where redU genes were introduced into various strains.

Since the gene product of SCO6673 has been suggested to be involved in the biosynthesis of CDA and its function has not previously been confirmed biochemically, this project looked at the essential modification catalyzed by the SCO6673 PPTase on the non-ribosomal peptidyl synthase peptidyl carrier proteins (PCPs) involved in CDA synthesis. This study confirmed with MALDI-TOF mass spectrometry, the modification of a CDA PCP by the SCO6673 PPTase. In addition, this project looked at the potential antagonistic relationship of the upstream SCO6672 gene with its hypothetical role in removing the phosphopantetheine cofactor from the holo-PCP. Using MALDI-TOF mass spectral analysis, this study was unable to detect the removal of the P-pant group by SCO6672. However, results were inconclusive and warrant further study.

Finally, this project took an initial look at the flux through the primary carbon metabolic pathways, glycolysis and the pentose phosphate pathway. A comparison of the enzymatic activity of select enzymes in these pathways was performed between the wild type and SCO6673 PPTase mutant strain. The enzymes tested include glyceraldehyde 3-phosphate dehydrogenase and pyruvate kinase in glycolysis, and glucose 6-phosphate dehydrogenase and transketolase from the pentose phosphate pathway. The carbon flux in both pathways increased in the mutant giving insight on how resources are used to overproduce undecylprodigiosin. The effects were greater in the pentose phosphate pathway with a general 2-fold increase in enzymatic activity. This is significant because the pentose phosphate pathway is a source of NADPH, the reducing agent used in making secondary metabolites.

We found 6 new effective ATRP catalysts that were faster than their bidentate counterparts, with an average conversion of 70% in 3 hours. We also found that minute alterations to the ligand structure resulted in marked differences in molecular weight control and reaction rate. Our structure-efficiency correlations showed that most of the observed trends are due to the ligand’s influence on the Cu(I)/Cu(II) equilibrium. Ligands with alkyl groups proximal to donor groups tended to effect faster polymerization rates and poorer molecular weight control than those without. Structurally flexible ligands tended to effect fast rates and very good molecular weight control. We believe that these observations are general, and can thus be used in the design of new ATRP catalysts.

Malaria is a parasitic disease that infects the human erythrocyte and feeds off its hemoglobin. Malaria is usually a mild disease often likened to a severe flu. However, one strain of the parasite, Plasmodium falciparum, has the ability to cause a deadly form of the disease known as severe malaria. A signature symptom of severe malaria is the appearance of rosettes, infected erythrocytes that adhere to uninfected erythrocytes thereby causing blockages in the microvasculature. Their appearance is caused by the binding of a parasitic protein from the infected erythrocyte to the carbohydrate based ABO blood antigens of an uninfected cell, particularly erythrocytes of blood groups A and B. The premise of this thesis is to create glycomimetic structures that provide the same or similar multivalent interactions of blood group A or B available to the protein. A first generation dendrimer based on bis-MPA has been successfully synthesized in this lab. The monosaccharide linkers to functionalize the dendrimers have been synthesized up to the glycosylation step thus introducing the variable length carbon-chain using the blood group B monosaccharide starting material, galactose. We have found that a direct glycosylation using borontrifuoride as an activating agent works equally well for two of the monosaccharides, galactose and glucosamine (the negative control), and each carbon linker so far. Further chemistry must be done to complete the synthesis of the linker components, including separation of the protected glucosamine linkers and synthesis of the blood group A linker starting from galactosamine. Fulfillment of these syntheses will provide the functional components needed to prepare the necessary dendrimer glycomimetics that can then be characterized for their biological abilities.

α,β-Unsaturated δ-lactones are a common structural motif in biologically active natural products. These structures can be found in a variety of compounds, including leptomycin B, jerangolid D and the kavalactone family. All of these compounds exhibit interesting medicinal effects, making the need for an efficient, general method to synthesize enantiopure α,β-unsaturated δ-lactones a priority. Past synthetic efforts in the literature to produce enantiopure α,β-unsaturated δ-lactones rely mainly on ring-closing metathesis and asymmetric catalysis methods. However, both of these methods have their limitations, particularly in the scope of the reaction.

In addition, intercepting this reaction after the triflation step also provides direct access to enantiopure vinyl triflates, which have been shown by Dudley to undergo fragmentation to provide an expeditious route to enantiopure homopropargyl alcohols. These homopropargyl alcohols can be used toward the asymmetric synthesis of natural products containing complex polyketide and macrolide structures. Further research is needed, however, to optimize formation of the triflates.

Through a collaboration with Dr. Andria Agusta of LIPI in Indonesia, the Richardson lab received five plant extracts, which had demonstrated antibiotic properties from previous studies in Indonesia. The Richardson lab hoped to investigate these plant extracts and deduce what compound(s) in them created the observed antibiotic effect. During the previous summer, preliminary research had been conducted on these plant extracts in order to create an effective methodology for bioactivity investigation.

In this thesis, H2-22 (Sageraea sp.), one of the five extracts provided by Dr. Agusta, was studied to discover the source of its bioactivity. Initial solvent fractionation was employed on the crude plant extract to begin separation of the extract into more manageable components. Further separation was achieved using Flash Column Chromatography (FCC) in order to isolate the bioactive fractions of the extract. The bioactivity of each component was monitored using a bioassay called bioautography along with corresponding TLC analysis for reference. Two major fractions, hexanes and MeOH, were isolated. The hexanes fraction was examined via GC/MS and NMR, however, it was discovered that the biologically-active compounds contained in this section were not novel. The MeOH fraction was purified extensively and it provided a single bioactive material, which was then submitted to the University of Nebraska Mass Spectroscopy lab for high resolution mass spectral analysis. Due to time constraints no further research could be performed on this fraction.

In order to prove the stereochemistry of the highly cytotoxic marine natural product tedanolide C, four macrolide model systems were designed with varying stereochemical arrangements at the C₁₀ and C₁₁–C₁₇ stereocenters. These model systems represent all possible stereochemical configurations of the C₁₀–C₁₇ backbone, maintaining the macrolide core of the natural product while truncating the C₁₇–C₂₃ side chain. Their spectroscopic comparison with tedanolide C should reveal the true stereochemistry of the natural product. A rapid, flexible synthesis of the C₁–C₁₁ fragment of tedanolide C was obtained in seven steps and unoptimized 7.9% yield from commercially available N-propionyl-(S)-isopropyl thiazolidinethione. Reagent-based control using a late-stage catalytic asymmetric hydroformylation reaction was used to access either C₁₀ epimer of the tedanolide macrolide models.

Streptomyces coelicolor is a model species for the genus of gram-positive, soil-dwelling bacteria with a complex life cycle involving multicellular differentiation, sporulation and antibiotic production. The stress response sigma factor, σ^U, in S. coelicolor is not well-characterized, but is believed to be regulated by its cognate anti-sigma factor RsuA and can be activated by acidic pH. Due to the homology between σ^Wregulation in B. subtilis and what is known about σ^Uregulation in S. coelicolor, the protein encoded by the SCO4110 (prsU) gene is hypothesized to be a putative protease that regulates σ^U by cleaving RsuA. To investigate the hypothesized regulation of σ^U by PrsU, two mutant reporter strains were created that lacked the prsU gene. These two prsU mutant reporter strains were assayed to determine the levels of σ^U activity by monitoring the GFP fluorescence or growth on kanamycin. In the GFP reporter assay, the prsU mutant presented with mid-level fluorescence that was less than the positive control but more than the negative control thus suggesting some σ^U activity is present in the prsU mutant. In the neo reporter assay, the prsU mutant also presented low levels of cell growth that was much less than the positive control. These results support that the putative protease PrsU is likely involved in the activation of σ^U, but does not corroborate the hypothesis that it is solely responsible for σ^Uactivity. That is, PrsU is involved in the regulation of σ^U, but there may be an alternate mechanism for activation of σ^U-dependent genes in S. coelicolor that is currently unknown.

In this work I develop methods to synthesize a family of deuteroflurocarbons (DFCs), which are a deuterated version of hydrofluorocarbons. Specifically, I use these methods to synthesize 1,1,1,2,2,3,3,4,4-nonafluoro-4-deuterobutane (1D-nfb) and 1,1,1,2,2,3,4,4,4-nonafluoro-3-deuterobutane (2D-nfb), with deuterofluoropentanes and deuterofluoropropanes as longer-range targets. A method had been developed [1] for the synthesis of 1D-nfb and this thesis improves this method in order to produce these molecules with higher yield and purity. The synthesis of 1D-nfb was taken as a general case for the synthesis of the family of deuterofluorocarbons. The level of purity for each trial was assessed by gas chromatography/ mass spectrometry analysis, 1H- and 19F-NMR. All the syntheses involve a single H/D exchange. The motivation for the synthesis of these molecules is their use for a number of applications, including spectroscopic studies of the structure and dynamics of hydrofluorocarbons. Since the known methods for the synthesis of DFCs are very limited or extremely expensive, this thesis develops methods to produce these compounds more easily and cheaply. The use of D2O, rather than CD3OD, as a deuterium source for the compounds greatly reduces the costs of the synthesis. A direct approach is developed for the synthesis of these molecules, which allows for a more efficient preparation. The method of heating (9-17 hrs) with a 1:69 molar ratio of the iodofluorocarbon precursor (1,1,1,2,2,3,3,4,4-nonafluoro-4-iodobutane) to D2O was determined to be the best method to synthesize 1D-nfb. A limited number of trials were conducted to synthesize 2D-nfb, but similar to the synthesis of 1D-nfb, the method of heating (9-17 hrs) with a 1:69 molar ratio of the iodofluorocarbon precursor (1,1,1,2,2,3,4,4,4-nonafluoro-3-iodobutane) to D2O provided the most satisfactory results. In the future, these results can be used to replace iodine with deuterium in any suitable substrate.

Neurosteroids are a class of steroids produced de novo in the brain that directly modify the action of neurotransmitters by binding to allosteric sites on their membrane receptors. The ∆ 4-3-ketosteroid allopregnanolone is a neurosteroid with potent anxiolytic effects due to its positive modulation of GABA_A receptors. Using an animal model of selective breeding for an infantile affective trait, high and low rates of neonatal ultrasonic vocalizations (USVs), the role of allopregnanolone synthesis and regulation in anxiety behavior was explored in this study. High line rats have been reported to have significantly lower levels of the neurosteroid in combined hippocampus and amygdala than Low line rats. This study examined differential expression of three enzymes involved in the rate-limiting steps of allopregnanolone synthesis: steroidogenic acute regulatory protein (StAR), a subunit of the peripheral benzodiazepine receptor (PBR) called translocator protein (TSPO), and 5α-reductase I (5αRI), as measured by protein and mRNA expression in hippocampus. While this study replicated Line differences in anxiety-like behavior using multiple measures of the open field task, no significant effects of Line were found on protein or mRNA expression of these three enzymes, suggesting that allopregnanolone regulation is not directly mediated by steroidogenic enzyme expression in hippocampus. However, there was a significant effect of sex on the mRNA expression of Tspo, suggesting that this enzyme might play a role in regulating the fluctuating levels of allopregnanolone over the course of the female estrous cycle.

Two Indonesian plant extracts, Irvingia sp. and Xylocarpus sp., supplied to us by Dr. Andria Agusta of the Indonesian Institute of Sciences (LIPI), were analyzed for their antibacterial activity against wild-type Bacillus subtilis YB886 and wild-type Escherichia coli K12. Both of these plant extracts have already been noted by ethnobotanical research for their biological activity. Rigorous isolation and purification of one compound from the 90% aqueous methanol fraction of Irvingia yielded a novel pentacyclic antibacterial compound whose molecular formula we believe to be C₃₄H₅₆O₈ based upon preliminary structural analysis.

The isolation of this novel compound was made using a bioassay-guided fractionation procedure that we had adapted from existing literature and then developed for use in the Richardson Lab. The foundation of this procedure was a bioassay called bioautography. It enabled us to visualize the antibacterial components of a particular fraction of a plant extract directly upon a TLC plate. Once localized, flash column chromatography was used to isolate bioactive compounds of interest. Structural characterization was completed using GC-MS spectrometry in Electron-Impact Ionization and Chemical-Ionization mode, as well as ¹H-, ¹³C-, and 2D^-1H/¹³C-NMR spectroscopic methods.

COMPUTER SCIENCE

The microfacet model of bidirectional reflectance distribution functions underlies most computer graphics rendering algorithms. It was derived from (selective) physics first principles and has been demonstrated to match real-world phenomena under manually tuned parameters. However, microfacets have never been verified to produce accurate macroscopic (visual-scale) results from real micrometer-scale geometry or to predict accurate microgeometry from real macroscopic measurements. In this paper, we will evaluate whether the microfacet model is physically accurate within measurement error for everyday materials.

Markov logic networks are a recently developed knowledge representation capable of compactly representing complex relationships and handling uncertainty in a principled manner. The deep transfer algorithm of Davis and Domingos proposes a method for learning the structure of an MLN by incorporating cross-domain knowledge — for example, using the relationships between yeast proteins to inform predictions about relationships in the movie business. This thesis explores several questions related to this algorithm and to cross-domain transfer in general. I first develop methods for simultaneous transfer from multiple domains, and propose that much of the success of deep transfer may be explained by a small number of commonly occurring structural properties, e.g. symmetry and transitivity. I then demonstrate empirically that deep transfer often performs best when using the target domain as its own transfer source, e.g. the most effective way to predict relationships in the movie business is to examine other relationships in the movie business. This suggests a reinterpretation of the deep transfer algorithm as a method for single-domain structure learning. Finally, I describe a new algorithm for cross-domain transfer which transfers a more specific form of structure than the second-order cliques used by Davis and Domingos, and show empirically that my approach performs competitively to the deep transfer algorithm, despite using a less sophisticated form of learning in the source domain.

GEOSCIENCES

Makushin Volcano is an active stratovolcano on Unalaska Island in the Aleutians. Previous studies have examined Holocene pyroclastics and pre-Holocene flows from Makushin, but as part of the Unalaska Keck Project during the summer of 2009 we found a pre-Holocene pyroclastic deposit, the Point Tebenkof ignimbrite. The Point Tebenkof ignimbrite is a 42-meter thick, unwelded, relatively mafic ignimbrite on the northern coast of the island to the west of Driftwood Bay. It is the oldest known pyroclastic deposit (>139 ka) and as such is a link to understanding the sequence of effusive vs. explosive Makushin eruptions. This study describes the ignimbrite and the overlying Red Cinder Dome flows based on their field characteristics and petrography. Electron microprobe data from the Point Tebenkof ignimbrite scoria were used for thermobarometry calculations after Putirka (2008) using clinopyroxene-glass and orthopyroxene-glass pairs.

Field descriptions reveal four visibly distinct layers in the Point Tebenkof ignimbrite. Based on similarities among samples in mineralogy and thermobarometry, it appears that the entire ignimbrite formed from the eruption of a magma chamber with a relatively constant temperature and pressure. Specifically, geothermometry data support a temperature of 950 -1040°C and most likely 970-1015°C. Although geobarometry data are more scattered, they suggest a pressure at or below 2 kbar, or within 6-7 km of the surface. The formation of the Point Tebenkof ignimbrite from a phreatomagmatic Plinian eruption in the Pleistocene reveals that Makushin shifted eruption styles earlier than was previously thought and explosively erupted large amounts of pyroclastic material from a shallow, ~1000°C magma chamber.

In July 2009, we recovered a varved sediment core from 35 m in the deep main basin of Linnévatnet, a high Arctic glacial lake in Svalbard. Arctic lakes are key locations for studying climate records because the Arctic is highly sensitive to climate change and because varves reflect seasonal and annual sedimentation rates. Previous research in Linnévatnet has focused primarily on the proximal basin near the Linnéelva (Linné River) inlet where it is difficult to distinguish annual sediment layers from event-based layers. The lake core analysis will therefore contribute to our understanding of the sediment stratigraphy in the deep main basin where varves reflect annual sedimentation.

To make a proxy climate record, we compared varve thickness to summer temperature, summer precipitation, winter precipitation, and glacier mass balance from the instrumental record. Summer temperature and summer precipitation show a statistically significant positive correlation with varve thickness, though with a low coefficient of determination (r²). We used thickness and a regression equation to estimate climate pre-dating the instrumental record. If higher summer temperatures and increased precipitation are related to thicker varves, then summer temperature and precipitation have been greater in the 20^th Century than in the past 1,000 years, and climate change in the 20^th Century has been greater than during the Little Ice Age and the Medieval Warm Period.

Ecological succession can be read through fossil reefs, recreating the story of how the reef communities established themselves and developed over time. It also reveals how they may have responded to damage, particularly from storm events, and how they recovered afterwards. As a result, succession in the fossil record can provide insight for modern day reef study, tracing long-term changes that are difficult to see in the study of living reefs. If environmental conditions at points in the past were similar to today’s, a direct comparison can be made. Such is the case with reefs that developed in the Gulf of California during the Late Pleistocene.

Reef succession, from the stabilization of a cobble substrate to the development of a diverse invertebrate community, is observed and documented through two of four Pleistocene fringing reefs that established off the southwest coast of Isla Cerralvo, Baja California Sur. The reefs, built by corals Porites panamensis and Pocillopora sp., were short-lived; each was covered over with algae-encrusted, elongate (sphericity: 0.6) cobbles during storm events. However, after the cobbles deposited, they were oriented (mean long axis: N2˚W) and locked in place, becoming a stable pavement suitable for colonization by corals. Each cobble layer subsequently supported the establishment of a new reef. Of five such cycles of cobbles and corals, only two (the 2nd and 3rd) show sufficient lateral continuity to be analyzed confidently. This study focuses on those two cycles. Census counts, cobble orientations and rind measurements of each cycle were documented in order to characterize succession from cobble/rhodolith pavements to mature coral reefs.

Most clasts within the cobble layers exhibit encrustation on all sides, suggesting the clasts were initially mobile. However, uneven encrustation suggests only occasional movement. After the clasts stabilized, coralline algae continued to grow, supporting coral recruitment. Clasts in the 2nd cycle (mean dimensions: 7.4 x 4.6 cm) have algal rinds that average 5 mm (Standard Deviation: 4 mm) at their thickest and 1 mm (SD: 1 mm) at their thinnest. They were colonized and overgrown by corals that average 16.2 cm in height. The corals within the reef are predominantly P. panamensis, (ratio to Pocillopora sp., 2.75:1) but during the colonization stage, there were likely more Pocillopora. Likewise, clasts within the 3rd cycle (mean dimensions: 7.2 x 4.6 cm) have rinds that average 3 mm (SD: 3 mm) at their thickest and 1 mm (SD: 1 mm) at their thinnest, later colonized and overgrown by corals that average 15.4 cm in height. The overlying reef layer is dominated by P. panamensis as well (ratio with Pocillopora sp., 9.3:1). From the top of the third cycle, P. panamensis is densely packed (14:1 against Pocillopora sp.), reflecting a shift towards a Porites-dominant climax stage within the reef. However, domination never occurred in this reef or any other in the section because succession reset through storm events before a climax stage could be reached.

The life of the reef, from establishment to death, is contained within a closed geologic system. First, sediment is washed out of the local arroyos during storm events, and deposited into the Gulf. Second, the strong winter winds and waves truncate the sedimentary fans and move sedimentary material south along the coast while the clasts accumulate algal rinds. Third, when another storm enters the gulf, the encrusted cobbles are rolled towards the island and lock in an orientation perpendicular to the SW-NE waves. Thus, local systems influenced both the stabilization and the eventual death of the coral layers.

As for the survival of the reef along an exposed shoreline, much credit goes to crustose coralline algae. They played a fundamental role in the sequence of reef succession and in creating strong reef frameworks. In the form of rhodoliths, coralline algae killed the old coral layers and helped stabilize the substrate. The encrusted substrate also likely aided in colonization and in cementing the reef proper. The resulting reefs were strong and generally resistant to the winter waves. This stands out from other reefs in the Gulf in that other reefs are found in more protected locations and do not employ coralline red algae in such a way. This suggests that coralline algae may be an important factor in reef survival on exposed coastlines in the Gulf, enabling reef growth where many organisms cannot survive. This calls to attention the importance of red algae in modern reef systems, particularly in the Gulf of California, where true reefs are now rare.

In landscapes where erosion rates exceed weathering, isolated bedrock outcrops may emerge as soil is removed. These outcrops, called tors, form when a heavily weathered area is subject to increased erosion rates, possibly due to dramatic climate shift. Mapping and measurements of tors in Gordon Gulch, a forested upland catchment in the northern Front Range of Colorado, shows that tor development is a function of erosion and weathering rates, bedrock characteristics, slope, and aspect. Satellite-based (GPS) measurements and geographic information system (GIS) analysis show that tor density and size are most closely related to the relative orientation of foliation with respect to local slope. Tors are much larger and more common on south-facing slopes because they are perpendicular to foliation of the gneissic units of the area, preventing downslope movement from taking advantage of weak layers.

Understanding the controls on tor evolution is an important step in studying how the Critical Zone (the area between fresh bedrock and the top of vegetation) evolves over time. Studying tors can reveal how rock properties and erosion processes control the response of slopes to events such as channel downcutting and climate change. Investigations of tors also help to reveal specific critical- zone processes, such as how regolith thickness affects tor and outcrop formation rates. In areas where local erosion rates exceed weathering rates, as in Gordon Gulch, tors can be an excellent indicator of geologically recent hillslope evolution.

MATHEMATICS AND STATISTICS

We present a generalized model of social networks using a weighted-edge graph with dynamics. Specifically, each edge in this model evolves in accordance with its membership in one or more triads, or edge triples; the stability of these triads will be defined by a dynamical interpretation of a variation of Balance Theory. We analyze this system in the single triad and general case, find several types of fixed points in the system, and point to directions for further study.

Consider a diagram as a four-valent graph on a sphere, that is, a graph where every vertex is adjacent to exactly four edges. We look at the faces of these diagrams as being m-gons when the face has exactly m edges. We consider what types of diagrams can be drawn that have their only faces be 2-gons or n-gons for some n≥5, how many of these diagrams exist, and how many components they can have. We then consider the same information for the case when all faces are either 3-gons or n-gons for n≥5.

A number of mathematical methods have been shown to model the zeroes of L-functions with remarkable success, including the Ratios Conjecture and Random Matrix Theory. In order to understand the structure of convolutions of families of L-functions, we investigate how well these methods model the zeros of such functions. Our primary focus is the convolution of the L-function associated to Ramanujan's tau function with the family of quadratic Dirichlet L-functions, for which J.B. Conrey and N.C. Snaith computed the Ratios Conjecture's prediction. Our main result is performing the number theory calculations and verifying these predictions for the one-level density up to square-root error term. Unlike Random Matrix Theory, which only predicts the main term, the Ratios Conjecture detects the arithmetic of the family and makes detailed predictions about their dependence in the lower order terms. Interestingly, while Random Matrix Theory is frequently used to model behavior of L-functions (or at least the main terms), there has been little if any work on the analogue of convolving families of L-functions by convolving random matrix ensembles. We explore one possibility by considering Kronecker products; unfortunately, it appears that this is not the correct random matrix analogue to convolving families.

Let (T,M) be a complete local ring with dimension at least one which contains the rationals, C a finite set of incomparable non-maximal prime ideals of T. We find sufficient conditions for T to be the completion of an excellent integral domain B₀ with semilocal generic formal fiber ring with maximal ideals the elements of C, and excellent reduced local rings B₁, B₂ ... B_k such that B₀ is contained in B₁ which is contained in B₂ and etc. We also require that B₁,...B_k have semilocal formal fiber rings, whose maximal ideals we can prescribe. In other words, we find a relatively weak sufficient conditions such that for a given complete local ring T we have an excellent integral domain B₀ and a chain of excellent reduced local rings B₁,...,B_k such that all of them complete to T and we have a containment as well as the properties concerning the formal fiber rings.

NEUROSCIENCE

Ischemic brain injury causes devastating and often permanent memory impairments. Estradiol has been implicated in reduction of ischemic brain damage; however, the underlying mechanisms of such neuroprotection remain unclear. The current study characterized estradiol neuroprotection in a mouse model of global ischemia. Furthermore, the role of estrogen receptor (ER) β in estradiol neuroprotection was assessed by using ER β knock out (ERβKO) mice. Female mice were ovariectomized and implanted with a capsule containing either oil or estradiol and subjected to ischemia via two-vessel occlusion (2VO). Mice were trained on the hippocampally-dependent contextual fear conditioning task. Dorsal hippocampal slices were stained using Fluorjade B (FJB) to identify degenerating cells. Wild type (WT) mice subjected to 2VO surgery showed impairment on the contextual memory task and showed an increase in FJB positive cells in the hippocampus. Estradiol reduced behavioral impairment and cellular degeneration of the hippocampus, specifically in the CA1. No behavioral impairment was evident in ERβKO mice that experienced 2VO. However, oil treated ERβKO mice suffered more ischemic damage in the CA1 than estradiol treated ERβKO mice. Contextual memory, though not correlated to total FJB positive cells, was associated with right CA1 damage in both WT and ERβKO mice. These finding suggest that estradiol protects against ischemia-induced cellular degeneration and functional memory impairments. Furthermore, the right hippocampus may be differentially involved in spatial memory. The role of ERβ remains unclear and may be differentially involved in estradiol mediated neuroprotection depending on the subregion involved. ERβKO mice were resistant to an ischemia-induced memory impairment and thus may be able to function on memory tasks despite cellular degeneration in the hippocampus.

Birdsong is currently the best animal model system for human speech. Previous research explored associations between brain space for song and salient features of the song, and in multiple songbird species showed that the number of syllables a bird sings is positively associated with the size of one song control nucleus, HVC. However, electrophysiological and lesion studies suggested that HVC plays a larger role than simply encoding distinct syllables. These studies linked HVC to the syntax, or ordering of the syllables. HVC size has not previously been compared to measures of sequence complexity or syllable structure, and the sizes of other nuclei involved in song production, Uva, RA, and LMAN, were not reliably associated with any song measure previously assessed. This study examines measures of syntax, syllable structure, and syllable repertoire size, and compares these to the carefully measured volumes of song control nuclei in Bengalese and zebra finches, two related ! species with marked differences in syntax complexity. Performing multiple regression modeling for nucleus size revealed that larger HVC volume is predicted by a larger syllable repertoire size, greater variability in syllable structure, and greater variability in the possible syllables ending a song bout. Larger Uva volume is predicted by a higher total number of syllables, fewer different syllables, and greater consistency in acoustic structure across renditions of the same syllable. There is also a significant positive association between Uva volume and a measure of repeats in Bengalese finches. Larger LMAN volume is predicted by lower entropy when syllable-to-stop transitions were excluded, lower syllable-to-stop entropy, and greater inter-syllable similarity. These models are discussed in the context of current research in the field.

Neurosteroids are a class of steroids produced de novo in the brain that directly modify the action of neurotransmitters by binding to allosteric sites on their membrane receptors. The ∆4-3-ketosteroid allopregnanolone is a neurosteroid with potent anxiolytic effects due to its positive modulation of GABAa receptors. Using an animal model of selective breeding for an infantile affective trait, high and low rates of neonatal ultrasonic vocalizations (USVs), the role of allopregnanolone synthesis and regulation in anxiety behavior was explored in this study. High line rats have been reported to have significantly lower levels of the neurosteroid in combined hippocampus and amygdala than Low line rats This study examined differential expression of three enzymes involved in the rate-limiting steps of allopregnanolone synthesis: steroidogenic acute regulatory protein (StAR), a subunit of the peripheral benzodiazepine receptor (PBR) called translocator protein (TSPO), and 5α-reductase I (5αRI), as measured by protein and mRNA expression in hippocampus. While this study replicated Line differences in anxiety-like behavior using multiple measures of the open field task, no significant effects of Line were found on protein or mRNA expression of these three enzymes, suggesting that allopregnanolone regulation is not directly mediated by steroidogenic enzyme expression in hippocampus. However, there was a significant effect of sex on the mRNA expression of TSPO, suggesting that this enzyme might play a role in regulating the fluctuating levels of allopregnanolone over the course of the female estrous cycle.

PHYSICS

A quantum computer, a computer based upon the manipulation of quantum systems, could solve many problems considered difficult for conventional computers. However, a quantum computer large enough to be useful would likely need to contain many distinct registers. Before such a quantum computer can be built, it must be possible to efficiently route quantum information (quantum states) from one register of the quantum computer to another, just as classical information is routed in a conventional computer. In this work we study the efficiency and faithfulness of parallel entanglement transfer on quantum networks. Once transferred, entanglement can be distilled and used to teleport arbitrary quantum states.

Anderson Localization, the phenomenon in disordered systems where there is a transition from extended to localized quantum states, has many important consequences in condensed matter physics. Perhaps most importantly, long-scale transport of particles will cease in systems exhibiting Anderson Localization. For this reason the localization transition is often referred to as a metal-insulator transition, as the disorder disrupts the transport of electrons and current can no longer flow. Another important development in condensed matter is the possibility of building quantum computers that can perform specific tasks exponentially faster than classical computers. In this thesis we will consider how diagonal disorder in the Hamiltonian affects the transport properties of particles on these graphs, with an eye toward the disorder’s effect on the speedup in the quantum algorithm.

The Standard Model predicts the properties and behavior of all observed particles to outstanding accuracy. However, it has a few theoretical short-comings which include the hierarchy problem and lack of a dark matter candidate. This has spurred the study of several theories which could resolve these issues. In this thesis we develop and test a strategy for using LHC data to detect the presence of multiple top or bottom partners T or B. Although our analysis is motivated by a model in which these particles are integer-spin scalars, it applies to any extension of the Standard Model with top or bottom partners.

Optical fiber is the backbone of modern high-speed telecommunications. Vast improvements over the past forty years have rendered fiber as the fastest and most reliable means of communication today. Optical fiber is a digital medium, as information is encoded in pulses within the fiber. The shorter the pulses can get, the faster information can be transferred. Pulses undergo all kinds of distortion in fiber and there is significant ongoing research to better understand pulse propagation with optical fiber. Our work specifically concerns using a nonlinear optical loop mirror (NOLM) to modelock a fiber laser for picosecond-pulsed operation.

It is a common assumption that because all stripe systems share the same smectic symmetry, all stripe patterns evolve in the same way. An experimental study on diblock copolymers stripe systems [8] has established stripe pattern ordering behavior that is assumed common to all stripe systems. To test this universality, we have begun a similar study using a diblock closely related to one used in the previous study. We have observed an ordering process that differs markedly from what was observed in the previous study, thus providing evidence that not all stripe patterns evolve in the same way. Methods of sample preparation, data acquisition, and data processing for measuring the kinetics and dynamics of thin film weakly-segregated (_XN ≈ 14) polystyrene-block-poly (methyl methacrylate) half-cylinder stripes were developed.

As semiconductor devices get smaller and smaller, the excitons in the semiconductors also get increasingly squeezed. As excitons play an important role in semiconductors it is important to understand the effects of confinement on the internal structure of excitons. The energy levels of excitons can be probed with radiation in the Terahertz regime (10¹²Hz). In our work we implement a system for producing coherent Terahertz radiation using an ultra-fast laser and photoconductive antennas. We measure the sensitivity and reproducibility of our system to determine that our system can be used to measure absorption effects and phase changes as small as 5% for the frequency range 0.5 to 1.6 THz. We also perform spectroscopy with fused silica to find that our measured value for the index of refraction agrees with the literature values within 2% for the frequency range 1 to 2 THz. We have a system ready to be used for the intended probing of excitonic energy levels.

We have developed a new algorithm to calculate phase-only holograms for application in Holographic Optical Trapping (HOT). This type of algorithm takes an input of desired trapping positions and relative trap intensities. It returns a set of phases (for the holograph) which will produce a good approximation of the desired trapping pattern. Having been designed to improve the performance of highly symmetric trapping patterns, this algorithm offers an 8% increase in efficiency and a 219% increase in uniformity over the existing Random Superposition (RS) algorithm for a 10 x 10 square lattice of traps. This is accomplished by adjusting tap phases to minimize fluctuations in the amplitude of the calculate ideal hologram plane. Monte Carlo sampling of the ideal hologram plane is necessary to keep runtime increases insignificant. This algorithm can be run prior to existing iterative algorithms such as Gerchberg-Saxton to give them significant performance improvements for a given number of iterations.

PSYCHOLOGY

The child anxiety literature suggests that mothers may direct their children’s attention towards threatening aspects of the environment, thereby placing them at risk for fear and anxiety. The current study sought to examine this mother-child dynamic during conversations about ambiguous hypothetical scenarios, and to investigate the behavioral and health-related correlates of the various interaction styles. Specifically, mother and child interpretive bias to threat behaviors were coded, ECG data were collected in-vivo to explore children’s levels of physiological arousal, and maternal report of child health and behavior problems were obtained. Results showed that, while children interpreted the situations as threatening more often than mothers, components of maternal interpretive bias to threat (IBT) behavior were associated with markers of childhood anxiety and physiological regulation. Specifically, children of mothers who initiated threatening interpretations had a profile of social difficulties, while children with mothers who expanded threatening interpretations more often displayed a more classically anxious profile. Maternal minimization of threat was associated with better child physiological regulation throughout the IBT paradigm. Several interaction effects provided evidence for an agonistic dyadic processes model of mother-child interpretive bias to threat, in which one member of the dyad expanded while the other minimized the threat. Particularly, when high-expanding mothers had high minimizing-children, the children showed a profile consistent with stress reactivity. Implications for future research examining the development and effects of mother-child interpretive bias are discussed.

There is a considerable body of research investigating the effects of stigma on people living with mental illnesses. However, this literature is largely focused on the effects of labels and conducted in the U.S. The present study aims to contribute a greater understanding of stigma by investigating the effects of important variables: the psychiatric label itself, target gender, and target agency in two different cultures. College students in the U.S. (n = 189) and high school students in Mexico (n = 90) were asked to read a vignette depicting a peer suffering from bipolar disorder, which is an increasingly common diagnosis among young people. In the 2x2x2 between-subjects design, three factors were systematically manipulated in the vignettes: whether the psychiatric label “bipolar” was used or not, the gender of the peer in the vignette, and the “agency” of the peer, i.e., whether the peer was an active vs. passive partner in his/her treatment. Participants then rated the targets on standard measures of social distance and stigmatizing attributions. Results generally showed low levels of stigmatizing attitudes in both samples. The effects of labeling are non-existent in Mexico and mild in the U.S., and the effects of target gender were negligible in the U.S. but significant in Mexico. The agency manipulation affected levels of stigma on various measures in both samples, such that high agency was associated with less stigmatizing, more benign ratings. The results suggest that stigma may be currently less severe than in previous studies, and that the construct of target agency is a fertile ground for future studies examining ways to reduce mental illness stigma.

Normative theories of decision-making require that people base their choices on the maximization of expected utility theory. However, Allais (1953) showed that people’s choices often deviate from the predictions of expected utility theory. In Allais experiments, people made choices between gambles where both the outcomes and the probabilities of those outcomes were numerically presented. This thesis aimed to determine whether Allais paradoxes occur in cases where the probabilities were not numerically given, but were learned instead from experiencing repeated outcomes. Participants learned the probabilities of the outcomes from experience in computerized tasks and then they were asked to make choices between gambles based on the learned probabilities. Of primary interest was whether people would still make choices that would conflict with the predictions of expected utility theory. The results showed that the participants on average learned the probabilities in the given tasks, and the Allais inconsistencies were diminished.

This study explores why some children defend peers who are being bullied, while others watch passively. We hypothesized that the phenomenon of pluralistic ignorance (PI), in which individuals’ behaviors are inhibited by misperceptions of the attitudes of their peers, might account for the difference between the behaviors of bystanders and defenders. We expected to find a negative association between PI and defending behavior, such that children who viewed themselves as more prosocial than their peers (high PI) would engage in less defending. In contrast, we expected to find a positive association between PI and passive bystander behavior. Finally, we explored how the trait of independence from peer norms might moderate the relationship between PI and bystander behavior. We surveyed 446 4th and 8th graders about their personal beliefs about bullying, their perceptions of their peers’ beliefs about bullying, their susceptibility to peer influence, and their behavioral roles in bullying situations. Contrary to expectations, we found no association between PI and passive bystander behavior, and a positive association between PI and defending behavior. While independence from norms did not moderate the relationship between PI and bystander behavior, several main effects emerged. Independence from norms was negatively associated with bullying and passive bystander behavior, and positively associated with defending behavior. Implications for intervention and future directions for research are discussed.

In this study, we examined the correlates of anxiety in a group of young adults with and without a history of parental cancer. Participants were young adults, primarily college students, who completed measures of anxiety, family relationships, and coping styles. Those participants with a history of parental cancer also completed questionnaires regarding social support, posttraumatic growth, and cancer-related communication. Results indicated that young adults with a history of parental cancer, particularly those whose parents died of cancer, were more anxious than participants with medically-healthy parents, as measured by both state and trait anxiety. Family relationships and coping styles did not moderate this relationship. Satisfaction with social support at the time of cancer diagnosis was associated with anxiety levels regardless of whether the participant’s parent survived or died of cancer. There was an interaction effect for appreciation of life, which moderated anxiety levels for the two cancer groups. Appreciation of life was positively correlated with anxiety among participants whose parents survived cancer, whereas it was negatively correlated for those whose parents died of cancer. The amount of information provided about the cancer and the approachability of the parents correlated with both state and trait anxiety. Clinical implications of these findings are discussed and directions for future research are explored.

Research into the unique behaviors associated with visual processing of faces has centered on the debate between the existence of a special face processing mechanism and a domain general system of expertise. Despite the wealth of literature in this field, face recognition ability is rarely treated in an incremental manner. The current study aims to explore variation in face recognition ability within a normally functioning population. Two distinct hypotheses are explored. First, the current experiment investigates the relationship between face recognition ability and prevalence of autistic traits. Secondly, the experiment aims to determine if increments of face recognition ability reflect optimization of gaze scanning for facial stimuli. In the first study, 147 subjects were administered a test of their face recognition ability and a measure of the degree to which they exhibit autistic traits. The results showed that autistic characteristics and social detriments in particular, were related to face processing ability. In the second study, gaze scanning paths of 47 subjects, divided into poor, average, and superior recognizers, were compared. The results showed no differences in gaze scan paths across ability groups. Implications of both findings are discussed.

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