A genetic screen to identify novel Helicobacter pylori virulence factors using Saccharomyces cerevisiae as a model eukaryotic cell

Helicobacter pylori is a spiral, gram-negative bacterium that colonizes the stomachs of approximately 50% of the World\u27s population overall and is a major etiological agent of human gastric adenocarcinoma. Of infected individuals, only 10-15% develop severe gastric disease due to environmental factors, host genetic factors, and more significantly, genetic differences in the infecting H pylori strains. Type I strains of H pylori contain a 40-kb cytotoxin-associated pathogenicity island (cag PAl) that encodes and secretes the CagA protein into host epithelial cells via a type IV secretion system. To date, CagA is the only identified effector protein of the cag PAI. The goal of this study was to identify novel H pylori virulence factors, to further elucidate their role in H pylori virulence and their potential as novel effectors of the cag PAI. In the work presented here, we generated an H pylori genomic plasmid library and screened this library in Saccharomyces cerevisiae for toxic effects. We initially identified 2 candidate H pylori virulence factors, however, after further analysis these candidates were not toxic to S. cerevisiae and are no longer genes of interest. To identify novel H pylori virulence factors, others in the lab are addressing pitfalls found in this study to conduct a better-structured screen that we believe will be successful in identifying H pylori genes of interest --Document

Galaxy gas flows inferred from a detailed, spatially resolved metal budget

We use the most extensive integral field spectroscopic map of a local galaxy, NGC 628, combined with gas and stellar mass surface density maps, to study the distribution of metals in this galaxy out to 3 effective radii ($\rm R_e$). At each galactocentric distance, we compute the metal budget and thus constrain the mass of metals lost. We find that in the disc about 50% of the metals have been lost throughout the lifetime of the galaxy. The fraction of metals lost is higher in the bulge ($\sim$70%) and decreases towards the outer disc ($\rm \sim 3 \ R_e$). In contrast to studies based on the gas kinematics, which are only sensitive to ongoing outflow events, our metal budget analysis enables us to infer the average outflow rate during the galaxy lifetime. By using simple physically motivated models of chemical evolution we can fit the observed metal budget at most radii with an average outflow loading factor of order unity, thus clearly demonstrating the importance of outflows in the evolution of disc galaxies of this mass range ($\rm log(M_\star/M_\odot) \sim 10)$. The observed gas phase metallicity is higher than expected from the metal budget and suggests late-time accretion of enriched gas, likely raining onto the disc from the metal-enriched halo.FB acknowledges support from the United Kingdom Science and Technology Facilities Council. This work makes use of THINGS (‘The Nearby Galaxy Survey’, Walter et al. 2008), HERACLES (the ‘HERA CO line Extragalactic Survey’, Leroy et al. 2009) and PINGS (the ‘PPAK IFS Nearby Galaxy Survey’, Rosales-Ortega et al. 2010). We acknowledge the contribution from the referee in improving the content and the clarity of the paper. We thank Fiorenzo Vincenzo and Francesca Matteucci for their invaluable help in interpreting the vast literature on chemical abundance modelling and nucleosynthetic yields. We also thank Ying-jie Peng for support and discussion on development of his chemical evolution models. We wish to thank Fabian Rosales-Ortega for kindly sharing the PINGS data on NGC 628 and for his encouragement and feedback on the early stages of this work. We thank Matt Auger for useful discussions and healthy skepticism and the participants to the MPIA summer workshop ‘A 3D view on galaxies evolution: from statistics to physics’ for insightful comments.This is the author accepted manuscript. The final version is available from Oxford University Press via http://dx.doi.org/10.1093/mnras/stv233

Leaf litter decomposition rates increase with rising mean annual temperature in Hawaiian tropical montane wet forests

Decomposing litter in forest ecosystems supplies nutrients to plants, carbon to heterotrophic soil microorganisms and is a large source of CO2 to the atmosphere. Despite its essential role in carbon and nutrient cycling, the temperature sensitivity of leaf litter decay in tropical forest ecosystems remains poorly resolved, especially in tropical montane wet forests where the warming trend may be amplified compared to tropical wet forests at lower elevations. We quantified leaf litter decomposition rates along a highly constrained 5.2 ◦C mean annual temperature (MAT) gradient in tropical montane wet forests on the Island ofHawaii. Dominant vegetation, substrate type and age, soil moisture, and disturbance history are all nearly constant across this gradient, allowing us to isolate the effect of rising MAT on leaf litter decomposition and nutrient release. Leaf litter decomposition rates were a positive linear function of MAT, causing the residence time of leaf litter on the forest floor to decline by ∼31 days for each 1 ◦C increase in MAT. Our estimate of the Q10 temperature coefficient for leaf litter decomposition was 2.17, within the commonly reported range for heterotrophic organic matter decomposition (1.5–2.5) across a broad range of ecosystems. The percentage of leaf litter nitrogen (N) remaining after six months declined linearly with increasing MAT from ∼88% of initial N at the coolest site to ∼74% at the warmest site. The lack of net N immobilization during all three litter collection periods at all MAT plots indicates that N was not limiting to leaf litter decomposition, regardless of temperature. These results suggest that leaf litter decay in tropical montane wet forests may be more sensitive to rising MAT than in tropical lowland wet forests, and that increased rates of N release from decomposing litter could delay or prevent progressive N limitation to net primary productivity with climate warming

SPT 0538–50: Physical Conditions in the Interstellar Medium of a Strongly Lensed Dusty Star-forming Galaxy at z = 2.8

We present observations of SPT-S J053816–5030.8, a gravitationally lensed dusty star-forming galaxy (DSFG) at z = 2.7817 that was first discovered at millimeter wavelengths by the South Pole Telescope. SPT 0538–50 is typical of the brightest sources found by wide-field millimeter-wavelength surveys, being lensed by an intervening galaxy at moderate redshift (in this instance, at z = 0.441). We present a wide array of multi-wavelength spectroscopic and photometric data on SPT 0538–50, including data from ALMA, Herschel PACS and SPIRE, Hubble, Spitzer, the Very Large Telescope, ATCA, APEX, and the Submillimeter Array. We use high-resolution imaging from the Hubble Space Telescope to de-blend SPT 0538–50, separating DSFG emission from that of the foreground lens. Combined with a source model derived from ALMA imaging (which suggests a magnification factor of 21 ± 4), we derive the intrinsic properties of SPT 0538–50, including the stellar mass, far-IR luminosity, star formation rate, molecular gas mass, and—using molecular line fluxes—the excitation conditions within the interstellar medium. The derived physical properties argue that we are witnessing compact, merger-driven star formation in SPT 0538–50 similar to local starburst galaxies and unlike that seen in some other DSFGs at this epoch

Eph receptors and ephrins in the developing chick cerebellum: relationship to sagittal patterning and granule cell migration

Spatiotemporal expression patterns of six members of the Eph gene family (EphA4, EphA3, EphB2, ephrin-B1, ephrin-A2, and ephrin-A5) were characterized immunocytochemically at various stages of chick cerebellar development. EphA4 expression is observed in the cerebellar anlage as early as embryonic day 5 (E5) and continues in the posthatch cerebellum. During the early period of cerebellar development (E3-E8), complementarity is observed between EphA4 and ephrin-A5 expression within the cerebellar-isthmal region. By E8, differential expression of EphA4 in parasagittal Purkinje cell bands is evident, and the expression remains banded in the posthatch cerebellum. Banded expression of the ephrin-A5 ligand complements EphA4 expression during the middle period (E9-E15). During this period, ephrin-A2 and EphA3 are coexpressed in a banded pattern and with variable correlation to EphA4. Variability in the banding expression is observed for EphA4, EphA3, ephrin-A5, and ephrin-A2 across different lobes, and graded complementarity in the expression pattern of EphA3 and ephrin-A5 is observed in the external granular layer between the posterior and anterior lobes. Analysis of Purkinje cell birth date in correlation with Eph-ephrin expression during the middle period reveals that early-born cells express EphA4, whereas late-born cells express ephrin-A5. Finally, EphA4 expression domains are respected by migrating granule cell ribbons, which express both ephrin-B1 and EphB2. These expression patterns suggest multiple roles for the Eph-ephrin system in cerebellar development, including demarcation/enforcement of boundaries of the cerebellar anlage, formation/maintenance of Purkinje cell compartments, and restriction of the early phase of granule cell migration to ribbons

The development and evaluation of exercises for meaningful responses in reading in grade two

Research chapter for this study will be found in Ash, Dorothea: "Development and evaluation of silent reading exercises in grade one" Thesis (M.A.)--Boston Universit