Doctor of Philosophy

dissertationPlatelets perform a critical role in both physiologic hemostasis and pathologic thrombosis, and the production and activation of platelets involves intricate regulation of cytoskeletal processes within these cells. A greater understanding of these cytoskeletal processes within platelets will offer the ability to manipulate them in hope of mitigating pathologies. In this dissertation I present a continuum of work progressing from the study of neural guidance cues in immune cells to neural guidance cues in platelet cytoskeletal function and finally to cytoskeletal alterations required for platelet production in thrombopoiesis. This work begins with the finding that, contrary to published reports, Slit2 does not regulate neutrophils directly, but instead acts through Robo4 to blunt endothelial hyper-response to cytokine storm. These studies led naturally into studies of guidance cues in other hematopoietic lineages, specifically platelets. I present data suggesting that Semaphorin 3E (Sema3E) inhibits all stages of platelet activation. Additionally, Sema3E reversibly inhibits platelet function by inactivating Rap1b, which is required for activation of llb 3 integrin. In attempts to determine the platelet receptor for Sema3E, using mice with a platelet-specific conditional deletion of the Sema3E receptor PlexinD1, I determined that PlexinD1 is not necessary for the platelet inhibitory activities of Sema3E. Simultaneously, in an attempt to produce Sema3E protein, I determined that effects originally attributed to Sema3E were in fact a result of Tween-20 contamination from commercially produced Sema3E formulation, thus terminating my studies of Semaphorins in platelets and suggesting the need for another look at the previously published reports of Sema3A in platelets. The study of cytoskeletal regulation in platelets lent naturally to the study of cytoskeletal functions in thrombopoiesis. Here I show that the proteasome inhibitor bortezomib causes thrombocytopenia by blunting platelet production in mice, consistent with clinical studies in humans. Furthermore, bortezomib prevents the production of proplatelets from megakaryocytes. I demonstrate that bortezomib treatment elevates both RhoA protein levels and RhoA activation in megakaryocytes and that inhibition of RhoA or its downstream kinase ROCK restores proplatelet production. As currently-approved drugs exist that inhibit both RhoA and ROCK, I suggest that these pathways are primary targets for treating bortezomib-induced thrombocytopenia

Delineation of a produced water plume in Pointe Coupee Parish, Louisiana

Three pits were excavated in the 1960’s at the Fordoche Oil Field in Lottie, Louisiana, as evaporation pits for oil well produced brines. The pits were closed and completed in the 1980’s. Previous studies indicate that produced water has leached into the subsurface within the area to the south and southeast of the pits. Ground penetrating radar (GPR) was utilized in an attempt to delineate the present location of the plume as well as test the feasibility of GPR within a clayey soil in south Louisiana. In addition to collection of GPR data, electrical conductivity logs and soil cores (including core sampling for sediment classification and chloride analysis) were collected. Electrical logs confirmed the presence of permeable zones interlaying impermeable zones. Core sampling for chloride confirmed the presence of the produced water within the study area. GPR was unsuccessful in delineating the plume at the site because of the high conductivity of the shallow sediments which inhibited penetration of radar waves. Calibration GPR studies were completed at grave sites in north and south Louisiana which proved successful due to favorable conditions

Resonant Orbits and the High Velocity Peaks Towards the Bulge

We extract the resonant orbits from an N-body bar that is a good representation of the Milky Way, using the method recently introduced by Molloy et al. (2015). By decomposing the bar into its constituent orbit families, we show that they are intimately connected to the boxy-peanut shape of the density. We highlight the imprint due solely to resonant orbits on the kinematic landscape towards the Galactic centre. The resonant orbits are shown to have distinct kinematic features and may be used to explain the cold velocity peak seen in the APOGEE commissioning data (Nidever at al., 2012). We show that high velocity peaks are a natural consequence of the motions of stars in the 2:1 orbit family and that stars on other higher order resonances can contribute to the peaks. The locations of the peaks vary with bar angle and, with the tacit assumption that the observed peaks are due to the 2:1 family, we find that the locations of the high velocity peaks correspond to bar angles in the range 10 < theta_bar < 25 (deg). However, some important questions about the nature of the peaks remain, such as their apparent absence in other surveys of the Bulge and the deviations from symmetry between equivalent fields in the north and south. We show that the absence of a peak in surveys at higher latitudes is likely due to the combination of a less prominent peak and a lower number density of bar supporting orbits at these latitudes.Comment: 7 Figures, 1 Table, Now includes figures & discussion of higher order resonances, Minor revisions to text throughout, Conclusions unchange

Resonant Clumping and Substructure in Galactic Discs

We describe a method to extract resonant orbits from N-body simulations exploiting the fact that they close in a frame rotating with a constant pattern speed. Our method is applied to the N-body simulation of the Milky Way by Shen et al. (2010). This simulation hosts a massive bar, which drives strong resonances and persistent angular momentum exchange. Resonant orbits are found throughout the disc, both close to the bar itself and out to the very edges of the disc. Using Fourier spectrograms, we demonstrate that the bar is driving kinematic substructure even in the very outer parts of the disc. We identify two major orbit families in the outskirts of the disc that make significant contributions to the kinematic landscape, namely the m:l = 3:-2 and 1:-1 families resonating with the pattern speed of the bar. A mechanism is described that produces bimodal distributions of Galactocentric radial velocities at selected azimuths in the outer disc. It occurs as a result of the temporal coherence of particles on the 3:-2 resonant orbits, which causes them to arrive simultaneously at pericentre or apocentre. This resonant clumping, due to the in-phase motion of the particles through their epicycle, leads to both inward and outward moving groups which belong to the same orbital family and consequently produce bimodal radial velocity distributions. This is a possible explanation of the bimodal velocity distributions observed towards the Galactic anti-Centre by Liu et al. (2012). Another consequence is that transient overdensities appear and dissipate (in a symmetric fashion) on timescales equal to the their epicyclic period resulting in a periodic pulsing of the disc's surface density.Comment: 11 Figures, 1 Table. Accepted for publication in ApJ. Version 2 reflects minor changes to the text. Animation referenced in Figure 7 is available at http://hubble.shao.ac.cn/~shen/resonantclumping/DensMovie.mp

Constraining local non-Gaussianities with kSZ tomography

Kinetic Sunyaev Zel'dovich (kSZ) tomography provides a powerful probe of the radial velocity field of matter in the Universe. By cross-correlating a high resolution CMB experiment like CMB S4 and a galaxy survey like DESI or LSST, one can measure the radial velocity field with very high signal to noise over a large volume of the universe. In this paper we show how this measurement can be used to improve constraints on primordial non-Gaussianities of the local type. The velocity field provides a measurement of the unbiased matter perturbations on large scales, which can be cross-correlated with the biased large-scale galaxy density field. This results in sample variance cancellation for a measurement of scale-dependent bias due to a non-zero $f_{NL}$. Using this method we forecast that CMB S4 and LSST combined reach a sensitivity $\sigma_{f_{NL}} \sim 0.5$, which is a factor of three improvement over the sensitivity using LSST alone (without internal sample variance cancellation). We take into account critical systematics like photometric redshifts, the kSZ optical depth degeneracy, and systematics affecting the shape of the galaxy auto-power spectrum and find that these have negligible impact, thus making kSZ tomography a robust probe for primordial non-Gaussianities. We also forecast the impact of mass binning on our constraints. The techniques proposed in this paper could be an important component of achieving the theoretically important threshold of $\sigma_{f_{NL}} \lesssim 1$ with future surveys.Comment: 16 pages, 7 figure

False discovery rate regression: an application to neural synchrony detection in primary visual cortex

Many approaches for multiple testing begin with the assumption that all tests in a given study should be combined into a global false-discovery-rate analysis. But this may be inappropriate for many of today's large-scale screening problems, where auxiliary information about each test is often available, and where a combined analysis can lead to poorly calibrated error rates within different subsets of the experiment. To address this issue, we introduce an approach called false-discovery-rate regression that directly uses this auxiliary information to inform the outcome of each test. The method can be motivated by a two-groups model in which covariates are allowed to influence the local false discovery rate, or equivalently, the posterior probability that a given observation is a signal. This poses many subtle issues at the interface between inference and computation, and we investigate several variations of the overall approach. Simulation evidence suggests that: (1) when covariate effects are present, FDR regression improves power for a fixed false-discovery rate; and (2) when covariate effects are absent, the method is robust, in the sense that it does not lead to inflated error rates. We apply the method to neural recordings from primary visual cortex. The goal is to detect pairs of neurons that exhibit fine-time-scale interactions, in the sense that they fire together more often than expected due to chance. Our method detects roughly 50% more synchronous pairs versus a standard FDR-controlling analysis. The companion R package FDRreg implements all methods described in the paper

Restoring Native Plant and Pollinator Communities on New York City Green Roofs

Urban development has dramatically decreased habitat for native plants and other wildlife. One of the native insect groups affected by this change are the bees and wasps (Order: Hymenoptera), which provide valuable ecosystem services like pollination of crops and ornamental plants. These insects are experiencing rapid population declines in urbanizing areas. A major obstacle to restoring pollinator populations in cities is the scarcity of space available that can be managed as habitat. A potential solution to this is to create patches of native vegetation on green roofs. Green roofs consist of live plants, growing media, and a drainage layer on top of a waterproof membrane. Most green roofs are planted with a mixture of non-native succulent plants (mostly from the genus Sedum), which are favored for their high survivorship and low maintenance requirements. On roofs with somewhat deeper media, a greater diversity of plants, including native plants typical of local grasslands, can persist. Here, we report on the differences in abundance and diversity of Hymenoptera attracted to native green roofs, Sedum green roofs, non-vegetated roofs, and ground-level green spaces. Preliminary data indicate extensive insect use of green roofs, with higher abundances on roofs planted with native species. The next phase of this research will involve comparing how the landscape context provided by different neighborhoods affects the development of the green roof biological communities

Key steps in the morphogenesis of a cranial placode in an invertebrate chordate, the tunicate Ciona savignyi

AbstractTunicates and vertebrates share a common ancestor that possessed cranial neurogenic placodes, thickenings in embryonic head epidermis giving rise to sensory structures. Though orthology assignments between vertebrate and tunicate placodes are not entirely resolved, vertebrate otic placodes and tunicate atrial siphon primordia are thought to be homologous based on morphology and position, gene expression, and a common signaling requirement during induction. Here, we probe key points in the morphogenesis of the tunicate atrial siphon. We show that the siphon primordium arises within a non-dividing field of lateral–dorsal epidermis. The initial steps of atrial primordium invagination are similar to otic placode invagination, but a placode-derived vesicle is never observed as for the otic vesicle of vertebrates. Rather, confocal imaging reveals an atrial opening through juvenile stages and beyond. We inject a photoactivatable lineage tracer to show that the early atrial siphon of the metamorphic juvenile, including its aperture and lining, derives from cells of the atrial placode itself. Finally, we perturb the routing of the gut to the left atrium by laser ablation and pharmacology to show that this adaptation to a sessile lifestyle depends on left–right patterning mechanisms present in the free-swimming chordate ancestor