Ecosystem legacies of invasive pines with exotic grasses and shrubs,

The aim of my thesis was to investigate the connection between invasive plants and the resident plant community via soil modification. Pines were chosen as the primary model invasive species for my project due to the dramatic transformations associated with pine invasions and local significance in Aotearoa | New Zealand. I began my research by leveraging soils from a previous experiment which involved various plant communities grown in the same steam sterilised soil. This provided known soil legacies to test various legacy factors associated with the previous plant communities and how those would affect the growth of future plants. For chapter two, I grew locally-relevant invasive species from three different functional groups, Pinus contorta (tree), Cytisus scoparius (shrub), and Holcus lanatus (grass) in a greenhouse experiment with these legacy soils. I found that legacies with a high proportion of exotic plants or with the presence of pine resulted in plants with the largest biomass. A potential biological mechanism was investigated by scoring nodules on Cytisus and mycorrhization on Pinus, which did not show a measurable effect across treatments. There were significant trends on fungal DNA sequences from pine seedling root samples, including showing that a pine legacy decreased the fungal community diversity while increasing pine seedling growth. Although the soil legacies for chapter two included invasive pine species in the legacy community, at most it was two seedlings in each growth phase, which might not have the same impact as soil from established adult trees or from various degrees of invasion. To address this issue, I sampled soil from along a pine invasional gradient, as measured by pine dominance. Also, I tested whether plant responses to the legacy soils differed if plants were grown individually or in communities; a closer representation of the natural system. This greenhouse study involved a community pot per sampling plot as well as an individual pot for each species represented in the community assay. An increasing pine legacy was found to be beneficial to most plants, but in a community context any benefit to native plants was obscured by the strong competitive fitness of many exotic species. Chapters two and three indicated that there was a biological effect in pine legacy soils, and that there was a reciprocal positive interaction between grasses and pines. Fungal endophytes were chosen as a biological indicator as they are associated with their host plant’s health and also will be affected by changes in resident soil. I collected grass roots (both exotic and native species) from paired plots (a pine invasion and a nearby uninvaded grassland). The endophytic fungal communities from exotic grasses and pine invasion sites had a greater abundance of potential pathogens, while sharing many generalists. This indicates a potential for spill over from exotic to native grasses, and that pine invasion soils might be a reservoir for pathogens. Exotic grass species might be better equipped to deal with these pathogens due to previous experience, compared to a lack of past interactions with native grass species, particularly if natives are under competitive stress. By demonstrating the effects of invasive pine legacy and various community legacy effects, my research could be helpful to land managers looking to control invasive pine spread. My thesis showed a pine soil legacy can be particularly beneficial to other exotic invasive species, which, in turn, can facilitate future invasions

Enhancing the Laser Scanning Confocal Microscopic Visualization of Lucifer Yellow Filled Cells in Whole-Mounted Tissue

The laser scanning confocal microscope (LSCM) is an extremely useful tool that allows fluorescently labelled cells to be visualized in whole-mount preparations. This is particularly advantageous, for example, in studying the dendritic trees of neurons with respect to their environment. One of the most popular, and easiest, ways to visualize a cell is to inject it intracellularly with the fluorophore Lucifer Yellow (LY). However, the argon gas lasers of most LSCM\u27s are not well matched to the excitation spectrum of aqueous LY. When this largely inappropriate excitation is combined with standard filters, designed for fluorescein fluorescence rather than Lucifer Yellow, the resulting image is poor. We report that clearing LY-injected neurons in methyl salicylate and mounting them in Entellan, a non-aqueous medium of high refractive index, enhances their visualization on a Bio-Rad LSCM with standard fluorescein (FITC) filters to an unexpected degree. This technique also leads to a substantial reduction in photobleaching

Titanium Doping of the Metallic One-Dimensional Antiferromagnet, Nb12O29

Monoclinic Nb12O29 undergoes a charge ordering transition to form antiferromagnetic Nb4+ chains (TN ~ 12 K) spaced 15.7 Å apart, which are coupled through mediation from a subset of metallic electrons which are present over all temperature regimes. We present the effects of disrupting the delicate electronic equilibrium in monoclinic Nb12O29 through doping Nb4+ (d1) with Ti4+ (d0) ions in the series, TixNb12−xO29. Powder neutron diffraction demonstrates that Ti is distributed over all of the 6 crystallographically distinct Nb positions. Magnetic susceptibility measurements reveal a rapid suppression of the magnetic ordered state on Ti doping, with a 3% percolation threshold consistent with the existence of one-dimensional Nb4+ chains. The reduction of the number of unpaired electrons on Ti4+ doping is shown to depopulate both localised and itinerant electron subsets, demonstrating that they are intrinsic to the properties of the system, which is argued to be a direct consequence of the mixture of bonding schemes within the lattice

The impact of direct-to-consumer personal genomic testing on perceived risk of breast, prostate, colorectal, and lung cancer: findings from the PGen study

Abstract Background Direct access to genomic information has the potential to transform cancer risk counseling. We measured the impact of direct-to-consumer genomic risk information on changes to perceived risk (ΔPR) of breast, prostate, colorectal and lung cancer among personal genomic testing (PGT) customers. We hypothesized that ΔPR would reflect directionality of risk estimates, attenuate with time, and be modified by participant characteristics. Methods Pathway Genomics and 23andMe customers were surveyed prior to receiving PGT results, and 2 weeks and 6 months post-results. For each cancer, PR was measured on a 5-point ordinal scale from “much lower than average” to “much higher than average.” PGT results, based on genotyping of common genetic variants, were dichotomized as elevated or average risk. The relationship between risk estimate and ΔPR was evaluated with linear regression; generalized estimating equations modeled this relationship over time. Results With the exception of lung cancer (for which ΔPR was positive regardless of result), elevated risk results were significantly associated with positive ΔPR, and average risk results with negative ΔPR (e.g., prostate cancer, 2 weeks: least squares-adjusted ΔPR = 0.77 for elevated risk versus −0.21 for average risk; p-valuedifference < 0.0001) among 1154 participants. Large changes were rare: for each cancer, <4 % of participants overall reported a ΔPR of ±3 or more units. Effect modification by age, cancer family history, and baseline interest was observed for breast, colorectal, and lung cancer, respectively. A pattern of decreasing impact on ΔPR over time was consistently observed, but this trend was significant only in the case of colorectal cancer. Conclusions We have quantified the effect on consumer risk perception of returning genetic-based cancer risk information directly to consumers without clinician mediation. Provided via PGT, this information has a measurable but modest effect on perceived cancer risk, and one that is in some cases modified by consumers’ non-genetic risk context. Our observations of modest marginal effect sizes, infrequent extreme changes in perceived risk, and a pattern of diminishing impact with time, suggest that the ability of PGT to effect changes to cancer screening and prevention behaviors may be limited by relatively small changes to perceived risk.http://deepblue.lib.umich.edu/bitstream/2027.42/114396/1/12920_2015_Article_140.pd

Design, methods, and participant characteristics of the Impact of Personal Genomics (PGen) Study, a prospective cohort study of direct-to-consumer personal genomic testing customers

Designed in collaboration with 23andMe and Pathway Genomics, the Impact of Personal Genomics (PGen) Study serves as a model for academic-industry partnership and provides a longitudinal dataset for studying psychosocial, behavioral, and health outcomes related to direct-to-consumer personal genomic testing (PGT). Web-based surveys administered at three time points, and linked to individual-level PGT results, provide data on 1,464 PGT customers, of which 71% completed each follow-up survey and 64% completed all three surveys. The cohort includes 15.7% individuals of non-white ethnicity, and encompasses a range of income, education, and health levels. Over 90% of participants agreed to re-contact for future research. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0096-0) contains supplementary material, which is available to authorized users

Is group cognitive behaviour therapy for postnatal depression evidence-based practice? A systematic review

Background: There is evidence that psychological therapies including cognitive behaviour therapy (CBT) may be effective in reducing postnatal depression (PND) when offered to individuals. In clinical practice, this is also implemented in a group therapy format, which, although not recommended in guidelines, is seen as a cost-effective alternative. To consider the extent to which group methods can be seen as evidence-based, we systematically review and synthesise the evidence for the efficacy of group CBT compared to currently used packages of care for women with PND, and we discuss further factors which may contribute to clinician confidence in implementing an intervention. Methods: Seventeen electronic databases were searched. All full papers were read by two reviewers and a third reviewer was consulted in the event of a disagreement on inclusion. Selected studies were quality assessed, using the Cochrane Risk of Bias Tool, were data extracted by two reviewers using a standardised data extraction form and statistically synthesised where appropriate using the fixed-effect inverse-variance method. Results: Seven studies met the inclusion criteria. Meta-analyses showed group CBT to be effective in reducing depression compared to routine primary care, usual care or waiting list groups. A pooled effect size of d = 0.57 (95% CI 0.34 to 0.80, p < 0.001) was observed at 10–13 weeks post-randomisation, reducing to d = 0.28 (95% CI 0.03 to 0.53, p = 0.025) at 6 months. The non-randomised comparisons against waiting list controls at 10–13 weeks was associated with a larger effect size of d = 0.94 (95% CI 0.42 to 1.47, p < 0.001). However due to the limitations of the available data, such as ill-specified definitions of the CBT component of the group programmes, these results should be interpreted with caution. Conclusions: Although the evidence available is limited, group CBT was shown to be effective. We argue, therefore, that there is sufficient evidence to implement group CBT, conditional upon routinely collected outcomes being benchmarked against those obtained in trials of individual CBT, and with other important factors such as patient preference, clinical experience, and information from the local context taken into account when making the treatment decision

Targeting Mycobacterium tuberculosis CoaBC through Chemical Inhibition of 4'-Phosphopantothenoyl-l-cysteine Synthetase (CoaB) Activity.

Coenzyme A (CoA) is a ubiquitous cofactor present in all living cells and estimated to be required for up to 9% of intracellular enzymatic reactions. Mycobacterium tuberculosis (Mtb) relies on its own ability to biosynthesize CoA to meet the needs of the myriad enzymatic reactions that depend on this cofactor for activity. As such, the pathway to CoA biosynthesis is recognized as a potential source of novel tuberculosis drug targets. In prior work, we genetically validated CoaBC as a bactericidal drug target in Mtb in vitro and in vivo. Here, we describe the identification of compound 1f, a small molecule inhibitor of the 4'-phosphopantothenoyl-l-cysteine synthetase (PPCS; CoaB) domain of the bifunctional Mtb CoaBC, and show that this compound displays on-target activity in Mtb. Compound 1f was found to inhibit CoaBC uncompetitively with respect to 4'-phosphopantothenate, the substrate for the CoaB-catalyzed reaction. Furthermore, metabolomic profiling of wild-type Mtb H37Rv following exposure to compound 1f produced a signature consistent with perturbations in pantothenate and CoA biosynthesis. As the first report of a direct small molecule inhibitor of Mtb CoaBC displaying target-selective whole-cell activity, this study confirms the druggability of CoaBC and chemically validates this target

CMB-S4 Science Book, First Edition

This book lays out the scientific goals to be addressed by the next-generation ground-based cosmic microwave background experiment, CMB-S4, envisioned to consist of dedicated telescopes at the South Pole, the high Chilean Atacama plateau and possibly a northern hemisphere site, all equipped with new superconducting cameras. CMB-S4 will dramatically advance cosmological studies by crossing critical thresholds in the search for the B-mode polarization signature of primordial gravitational waves, in the determination of the number and masses of the neutrinos, in the search for evidence of new light relics, in constraining the nature of dark energy, and in testing general relativity on large scales

The Far-Ultraviolet "Continuum" in Protoplanetary Disk Systems II: CO Fourth Positive Emission and Absorption

We exploit the high sensitivity and moderate spectral resolution of the $HST$-Cosmic Origins Spectrograph to detect far-ultraviolet spectral features of carbon monoxide (CO) present in the inner regions of protoplanetary disks for the first time. We present spectra of the classical T Tauri stars HN Tau, RECX-11, and V4046 Sgr, representative of a range of CO radiative processes. HN Tau shows CO bands in absorption against the accretion continuum. We measure a CO column density and rotational excitation temperature of N(CO) = 2 +/- 1 $\times$ 10$^{17}$ cm$^{-2}$ and T_rot(CO) 500 +/- 200 K for the absorbing gas. We also detect CO A-X band emission in RECX-11 and V4046 Sgr, excited by ultraviolet line photons, predominantly HI LyA. All three objects show emission from CO bands at $\lambda$ $>$ 1560 \AA, which may be excited by a combination of UV photons and collisions with non-thermal electrons. In previous observations these emission processes were not accounted for due to blending with emission from the accretion shock, collisionally excited H$_{2}$, and photo-excited H2; all of which appeared as a "continuum" whose components could not be separated. The CO emission spectrum is strongly dependent upon the shape of the incident stellar LyA emission profile. We find CO parameters in the range: N(CO) 10$^{18-19}$ cm$^{-2}$, T_{rot}(CO) > 300 K for the LyA-pumped emission. We combine these results with recent work on photo- and collisionally-excited H$_{2}$ emission, concluding that the observations of ultraviolet-emitting CO and H2 are consistent with a common spatial origin. We suggest that the CO/H2 ratio in the inner disk is ~1, a transition between the much lower interstellar value and the higher value observed in solar system comets today, a result that will require future observational and theoretical study to confirm.Comment: 12 pages, 7 figures, 3 tables. ApJ - accepte