From Single Proteins to the Proteome : Crosslinking Mass Spectrometry - a Simple Technique with Broad Implications

Protein-protein interactions are essential for cellular processes. Detection of protein-protein interactions on both a small scale and a whole-of-cell scale is crucial to understanding life. Many technologies have been developed to detect protein-protein interactions, but few are capable of detecting these on large scale under native conditions. Crosslinking-mass spectrometry has been used for some time to study protein-protein interactions on a small-scale (single protein to protein complexes) and has the potential for application to intact cells, resulting in large protein interaction networks. There are many considerations when adapting a small-scale technology to a large-scale system. This thesis aims to investigate these and present means by which they can be addressed. Firstly, two crosslinking-mass spectrometry pipelines are used to comprehensively examine the interaction between yeast enzyme Hmt1p methyltransferase and its substrate Npl3p, and the results from the pipelines are compared. Secondly, acquisition strategies learnt from the first study are used to examine a system involving crosstalk of protein post-translational modifications (PTMs). Protein Nop1p is studied with crosslinking-mass spectrometry to detect changes in interactions between phosphorylated Nop1p and Hmt1p methyltransferase, and methylated Nop1p and Sky1p kinase. Thirdly, knowledge generated from studies one and two is applied to a large-scale sample. Protein-correlation profiling and crosslinking-mass spectrometry are coupled and used to predict novel interactions from size-exclusion fractionated yeast lysate. Together these three studies address current gaps in the crosslinking-mass spectrometry field; they assess the confidence of identifications, use reduced sample complexity for increased identifications and determine how interactions controlled by PTMs can be studied

LEGUS Discovery of a Light Echo Around Supernova 2012aw

We have discovered a luminous light echo around the normal Type II-Plateau Supernova (SN) 2012aw in Messier 95 (M95; NGC 3351), detected in images obtained approximately two years after explosion with the Wide Field Channel 3 on-board the Hubble Space Telescope (HST) by the Legacy ExtraGalactic Ultraviolet Survey (LEGUS). The multi-band observations span from the near-ultraviolet through the optical (F275W, F336W, F438W, F555W, and F814W). The apparent brightness of the echo at the time was ~21--22 mag in all of these bands. The echo appears circular, although less obviously as a ring, with an inhomogeneous surface brightness, in particular, a prominent enhanced brightness to the southeast. The SN itself was still detectable, particularly in the redder bands. We are able to model the light echo as the time-integrated SN light scattered off of diffuse interstellar dust in the SN environment. We have assumed that this dust is analogous to that in the Milky Way with R_V=3.1. The SN light curves that we consider also include models of the unobserved early burst of light from the SN shock breakout. Our analysis of the echo suggests that the distance from the SN to the scattering dust elements along the echo is ~45 pc. The implied visual extinction for the echo-producing dust is consistent with estimates made previously from the SN itself. Finally, our estimate of the SN brightness in F814W is fainter than that measured for the red supergiant star at the precise SN location in pre-SN images, possibly indicating that the star has vanished and confirming it as the likely SN progenitor.Comment: 10 pages, 9 figures, to appear in the Astrophysical Journa

A machine learning approach using partitioning around medoids clustering and random forest classification to model groups of farms in regard to production parameters and bulk tank milk antibody status of two major internal parasites in dairy cows

Fasciola hepatica and Ostertagia ostertagi are internal parasites of cattle compromising physiology, productivity, and well-being. Parasites are complex in their effect on hosts, sometimes making it difficult to identify clear directions of associations between infection and production parameters. Therefore, unsupervised approaches not assuming a structure reduce the risk of introducing bias to the analysis. They may provide insights which cannot be obtained with conventional, supervised methodology. An unsupervised, exploratory cluster analysis approach using the k–mode algorithm and partitioning around medoids detected two distinct clusters in a cross-sectional data set of milk yield, milk fat content, milk protein content as well as F. hepatica or O. ostertagi bulk tank milk antibody status from 606 dairy farms in three structurally different dairying regions in Germany. Parasite–positive farms grouped together with their respective production parameters to form separate clusters. A random forests algorithm characterised clusters with regard to external variables. Across all study regions, co–infections with F. hepatica or O. ostertagi, respectively, farming type, and pasture access appeared to be the most important factors discriminating clusters (i.e. farms). Furthermore, farm level lameness prevalence, herd size, BCS, stage of lactation, and somatic cell count were relevant criteria distinguishing clusters. This study is among the first to apply a cluster analysis approach in this context and potentially the first to implement a k–medoids algorithm and partitioning around medoids in the veterinary field. The results demonstrated that biologically relevant patterns of parasite status and milk parameters exist between farms positive for F. hepatica or O. ostertagi, respectively, and negative farms. Moreover, the machine learning approach confirmed results of previous work and shed further light on the complex setting of associations a between parasitic diseases, milk yield and milk constituents, and management practices

Star Formation Histories of the LEGUS dwarf galaxies. II. Spatially resolved star formation history of the Magellanic irregular NGC 4449

We present a detailed study of the Magellanic irregular galaxy NGC 4449 based on both archival and new photometric data from the Legacy Extragalactic UV Survey, obtained with the Hubble Space Telescope Advanced Camera for Surveys and Wide Field Camera 3. Thanks to its proximity ($D=3.82\pm 0.27$ Mpc) we reach stars 3 magnitudes fainter than the tip of the red giant branch in the F814W filter. The recovered star formation history spans the whole Hubble time, but due to the age-metallicity degeneracy of the red giant branch stars, it is robust only over the lookback time reached by our photometry, i.e. $\sim 3$ Gyr. The most recent peak of star formation is around 10 Myr ago. The average surface density star formation rate over the whole galaxy lifetime is $0.01$ M$_{\odot}$ yr$^{-1}$ kpc$^{-2}$. From our study it emerges that NGC 4449 has experienced a fairly continuous star formation regime in the last 1 Gyr with peaks and dips whose star formation rates differ only by a factor of a few. The very complex and disturbed morphology of NGC 4449 makes it an interesting galaxy for studies of the relationship between interactions and starbursts, and our detailed and spatially resolved analysis of its star formation history does indeed provide some hints on the connection between these two phenomena in this peculiar dwarf galaxy.Comment: 16 pages, 25 figures. Accepted for publication in the Astrophysical Journa

Hierarchical Star Formation in Nearby LEGUS Galaxies

Hierarchical structure in ultraviolet images of 12 late-type LEGUS galaxies is studied by determining the numbers and fluxes of nested regions as a function of size from ~1 to ~200 pc, and the number as a function of flux. Two starburst dwarfs, NGC 1705 and NGC 5253, have steeper number-size and flux-size distributions than the others, indicating high fractions of the projected areas filled with star formation. Nine subregions in 7 galaxies have similarly steep number-size slopes, even when the whole galaxies have shallower slopes. The results suggest that hierarchically structured star-forming regions several hundred parsecs or larger represent common unit structures. Small galaxies dominated by only a few of these units tend to be starbursts. The self-similarity of young stellar structures down to parsec scales suggests that star clusters form in the densest parts of a turbulent medium that also forms loose stellar groupings on larger scales. The presence of super star clusters in two of our starburst dwarfs would follow from the observed structure if cloud and stellar subregions more readily coalesce when self-gravity in the unit cell contributes more to the total gravitational potential.Comment: 9 pages, 4 figures, accepted for ApJ

The Radial Distribution of the Interstellar Medium in Disk Galaxies: Evidence for Secular Evolution

One possible way for spiral galaxies to internally evolve would be for gas to flow to the center and form stars in a central disk (pseudo-bulge). If the inflow rate is faster than the rate of star formation, a central concentration of gas will form. In this paper we present radial profiles of stellar and 8 μm emission from polycyclic aromatic hydrocarbons (PAHs) for 11 spiral galaxies to investigate whether the interstellar medium in these galaxies contains a central concentration above that expected from the exponential disk. In general, we find that the two-dimensional CO and PAH emission morphologies are similar, and that they exhibit similar radial profiles. We find that in 6 of the 11 galaxies there is a central excess in the 8 μm and CO emission above the inward extrapolation of an exponential disk. In particular, all four barred galaxies in the sample have strong central excesses in both 8 μm and CO emission. These correlations suggest that the excess seen in the CO profiles is, in general, not simply due to a radial increase in the CO emissivity. In the inner disk, the ratio of the stellar to the 8 μm radial surface brightness is similar for 9 of the 11 galaxies, suggesting a physical connection between the average stellar surface brightness and the average gas surface brightness at a given radius. We also find that the ratio of the CO to 8 μm PAH surface brightness is consistent over the sample, implying that the 8 μm PAH surface brightness can be used as an approximate tracer of the interstellar medium

Insulin, Hyperglycemia, and Severe Retinopathy of Prematurity in Extremely Low-Birth-Weight Infants

Objective This study aims to determine the association between hyperglycemia, insulin therapy, and severe retinopathy of prematurity (ROP) in extremely low-birth-weight (ELBW) infants. Study Design In this retrospective database study, we included all ELBW infants who were 180 mg/dL. Covariates were GA, small for GA status, discharge year, sex, Apgar score at 5 minutes, mechanical ventilation, oxygen use, bacteremia, and postnatal steroid exposure. We defined severe ROP as ROP requiring bevacizumab, cryotherapy, laser therapy, or vitrectomy. Sensitivity analysis using BG > 150 mg/dL and > 200 mg/dL was performed. Results A total of 24,548 infants were included; 2,547 (10%) had severe ROP. Hyperglycemia alone was not associated with severe ROP (odds ratio [OR], 0.88; 95% confidence interval [CI], 0.66-1.17). Hyperglycemia and insulin use were not associated with severe ROP (OR, 1.43; 95% CI, 0.91-2.23). BG > 150 mg/dL and insulin use were associated with severe ROP (OR, 1.34; 95% CI, 1.02-1.76). Conclusions Hyperglycemia alone was not associated with severe ROP in ELBW infants. However, we did observe a possible trend between the use of insulin and severe ROP.National Center for Advancing Translational Sciences of the National Institutes of Health (NIH)U.S. governmentNational Institute of Child Health and Human DevelopmentNIHNational Center for Advancing Translational Sciences of the NIHU.S. Food and Drug AdministrationCempra PharmaceuticalsDuke Univ, Dept Pediat, Sch Med, Durham, NC 27706 USADuke Univ, Sch Med, Duke Clin Res Inst, Durham, NC USAKK Womens & Childrens Hosp, Childrens Intens Care Unit, Singapore, SingaporeUniv Fed Sao Paulo, Ecola Paulista Med, Div Neonatal Med, Sao Paulo, BrazilUniv N Carolina, Dept Pediat, Chapel Hill, NC USAMEDNAX Inc, Pediat Med Grp, Jacksonville, FL USAUniv Fed Sao Paulo, Ecola Paulista Med, Div Neonatal Med, Sao Paulo, BrazilNIH: UL1TR001117U.S. government: HHSN267200700051CNational Institute of Child Health and Human Development: K23HD068497National Institute of Child Health and Human Development: HHSN275201000003INational Institute of Child Health and Human Development: 1R01-HD081044-01National Center for Advancing Translational Sciences of the NIH: UL1TR001117U.S. Food and Drug Administration: 1R18-FD005292-01Cempra Pharmaceuticals: HHS0100201300009CWeb of Scienc

Insulin, Hyperglycemia, and Severe Retinopathy of Prematurity in Extremely Low-Birth-Weight Infants

To determine the association between hyperglycemia, insulin therapy, and severe retinopathy of prematurity (ROP) in extremely-low-birth-weight (ELBW) infants

Candidate LBV stars in galaxy NGC 7793 found via HST photometry + MUSE spectroscopy

Only about 19 Galactic and 25 extragalactic bonafide luminous blue variables (LBVs) are known to date. This incomplete census prevents our understanding of this crucial phase of massive star evolution which leads to the formation of heavy binary black holes via the classical channel. With large samples of LBVs one could better determine the duration and maximum stellar luminosity which characterize this phase. We search for candidate LBVs (cLBVs) in a new galaxy, NGC 7793. For this purpose, we combine high spatial resolution images from two Hubble Space Telescope (HST) programs with optical spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE). By combining PSF-fitting photometry measured on F547M, F657N, and F814W images, with restrictions on point-like appearance (at HST resolution) and H α luminosity, we find 100 potential cLBVs, 36 of which fall in the MUSE fields. Five of the latter 36 sources are promising cLBVs which have MV ≤ −7 and a combination of: H α with a P-Cygni profile; no [O I]λ6300 emission; weak or no [O III]λ5007 emission; large [N II]/H α relative to H II regions; and [S II]λ6716/[S II]λ6731∼1⁠. It is not clear if these five cLBVs are isolated from O-type stars, which would favour the binary formation scenario of LBVs. Our study, which approximately covers one fourth of the optical disc of NGC 7793, demonstrates how by combining the above HST surveys with multi-object spectroscopy from 8-m class telescopes, one can efficiently find large samples of cLBVs in nearby galaxies

The emission by dust and stars of nearby galaxies in the Herschel KINGFISH survey

Using new far-infrared imaging from the Herschel Space Observatory with ancillary data from ultraviolet (UV) to submillimeter wavelengths, we estimate the total emission from dust and stars of 62 nearby galaxies in the KINGFISH survey in a way that is as empirical and model independent as possible. We collect and exploit these data in order to measure from the spectral energy distributions (SEDs) precisely how much stellar radiation is intercepted and re-radiated by dust, and how this quantity varies with galaxy properties. By including SPIRE data, we are more sensitive to emission from cold dust grains than previous analyses at shorter wavelengths, allowing for more accurate estimates of dust temperatures and masses. The dust/stellar flux ratio, which we measure by integrating the SEDs, has a range of nearly three decades (from 10(-2.2) to 10(0.5)). The inclusion of SPIRE data shows that estimates based on data not reaching these far-IR wavelengths are biased low by 17% on average. We find that the dust/stellar flux ratio varies with morphology and total infrared (IR) luminosity, with dwarf galaxies having faint luminosities, spirals having relatively high dust/stellar ratios and IR luminosities, and some early types having low dust/stellar ratios. We also find that dust/stellar flux ratios are related to gas-phase metallicity ((log(f(dust)/f(*)) over bar) = -0.66 +/- 0.08 and -0.22 +/- 0.12 for metal-poor and intermediate-metallicity galaxies, respectively), while the dust/stellar mass ratios are less so (differing by approximate to 0.2 dex); the more metal-rich galaxies span a much wider range of the flux ratios. In addition, the substantial scatter between dust/stellar flux and dust/stellar mass indicates that the former is a poor proxy of the latter. Comparing the dust/stellar flux ratios and dust temperatures, we also show that early types tend to have slightly warmer temperatures (by up to 5 K) than spiral galaxies, which may be due to more intense interstellar radiation fields, or possibly to different dust grain compositions. Finally, we show that early types and early-type spirals have a strong correlation between the dust/stellar flux ratio and specific star formation rate, which suggests that the relatively bright far-IR emission of some of these galaxies is due to ongoing (if limited) star formation as well as to the radiation field from older stars, which is heating the dust grains