Broad-Scale Redistribution of mRNA Abundance and Transcriptional Machinery in Response to Growth Rate in Salmonella Enterica Serovar Typhimurium

We have investigated the connection between the four-dimensional architecture of the bacterial nucleoid and the organism\u27s global gene expression programme. By localizing the transcription machinery and the transcriptional outputs across the genome of the model bacterium Salmonella enterica serovar Typhimurium at different stages of the growth cycle, a surprising disconnection between gene dosage and transcriptional output was revealed. During exponential growth, gene output occurred chiefly in the Ori (origin), Ter (terminus) and NSL (non-structured left) domains, whereas the Left macrodomain remained transcriptionally quiescent at all stages of growth. The apparently high transcriptional output in Ter was correlated with an enhanced stability of the RNA expressed there during exponential growth, suggesting that longer mRNA half-lives compensate for low gene dosage. During exponential growth, RNA polymerase (RNAP) was detected everywhere, whereas in stationary phase cells, RNAP was concentrated in the Ter macrodomain. The alternative sigma factors RpoE, RpoH and RpoN were not required to drive transcription in these growth conditions, consistent with their observed binding to regions away from RNAP and regions of active transcription. Specifically, these alternative sigma factors were found in the Ter macrodomain during exponential growth, whereas they were localized at the Ori macrodomain in stationary phase

The On/Off Nature of Star-Planet Interactions

Evidence suggesting an observable magnetic interaction between a star and its hot Jupiter appears as a cyclic variation of stellar activity synchronized to the planet's orbit. In this study, we monitored the chromospheric activity of 7 stars with hot Jupiters using new high-resolution echelle spectra collected with ESPaDOnS over a few nights in 2005 and 2006 from the CFHT. We searched for variability in several stellar activity indicators (Ca II H, K, the Ca II infrared triplet, Halpha, and He I). HD 179949 has been observed almost every year since 2001. Synchronicity of the Ca II H & K emission with the orbit is clearly seen in four out of six epochs, while rotational modulation with P_rot=7 days is apparent in the other two seasons. We observe a similar phenomenon on upsilon And, which displays rotational modulation (P_rot=12 days) in September 2005, in 2002 and 2003 variations appear to correlate with the planet's orbital period. This on/off nature of star-planet interaction (SPI) in the two systems is likely a function of the changing stellar magnetic field structure throughout its activity cycle. Variability in the transiting system HD 189733 is likely associated with an active region rotating with the star, however, the flaring in excess of the rotational modulation may be associated with its hot Jupiter. As for HD 179949, the peak variability as measured by the mean absolute deviation for both HD 189733 and tau Boo leads the sub-planetary longitude by 70 degrees. The tentative correlation between this activity and the ratio of Mpsini to the planet's rotation period, a quantity proportional to the hot Jupiter's magnetic moment, first presented in Shkolnik et al. 2005 remains viable. This work furthers the characterization of SPI, improving its potential as a probe of extrasolar planetary magnetic fields.Comment: Accepted for publication in the Astrophysical Journa

Improving pulsar-timing solutions through dynamic pulse fitting

Precision pulsar timing is integral to the detection of the nanohertz stochastic gravitational-wave background as well as understanding the physics of neutron stars. Conventional pulsar timing often uses fixed time and frequency-averaged templates to determine the pulse times of arrival, which can lead to reduced accuracy when the pulse profile evolves over time. We illustrate a dynamic timing method that fits each observing epoch using basis functions. By fitting each epoch separately, we allow for the evolution of the pulse shape epoch to epoch. We apply our method to PSR J1103$-$5403 and demonstrate that it undergoes mode changing, making it the fourth millisecond pulsar to exhibit such behaviour. Our method, which is able to identify and time a single mode, yields a timing solution with a root-mean-square error of 1.343 $\mu \mathrm{s}$, a factor of 1.78 improvement over template fitting on both modes. In addition, the white-noise amplitude is reduced 4.3 times, suggesting that fitting the full data set causes the mode changing to be incorrectly classified as white noise. This reduction in white noise boosts the signal-to-noise ratio of a gravitational-wave background signal for this particular pulsar by 32%. We discuss the possible applications for this method of timing to study pulsar magnetospheres and further improve the sensitivity of searches for nanohertz gravitational waves.Comment: Accepted in MNRAS, 8 pages, 8 figure

Genetic Regulation of Virulence and Antibiotic Resistance in Acinetobacter baumannii

Multidrug resistant microorganisms are forecast to become the single biggest challenge to medical care in the 21st century. Over the last decades, members of the genus Acinetobacter have emerged as bacterial opportunistic pathogens, in particular as challenging nosocomial pathogens because of the rapid evolution of antimicrobial resistances. Although we lack fundamental biological insight into virulence mechanisms, an increasing number of researchers are working to identify virulence factors and to study antibiotic resistance. Here, we review current knowledge regarding the regulation of virulence genes and antibiotic resistance in Acinetobacter baumannii. A survey of the two-component systems AdeRS, BaeSR, GacSA and PmrAB explains how each contributes to antibiotic resistance and virulence gene expression, while BfmRS regulates cell envelope structures important for pathogen persistence. A. baumannii uses the transcription factors Fur and Zur to sense iron or zinc depletion and upregulate genes for metal scavenging as a critical survival tool in an animal host. Quorum sensing, nucleoid-associated proteins, and non-classical transcription factors such as AtfA and small regulatory RNAs are discussed in the context of virulence and antibiotic resistance

Reproductive history differs by molecular subtypes of breast cancer among women aged ≤50 years in Scotland in 2009-16:A cross-sectional study

BACKGROUND: The aetiology of breast cancers diagnosed ≤ 50 years of age remains unclear. We aimed to compare reproductive risk factors between molecular subtypes of breast cancer, thereby suggesting possible aetiologic clues, using routinely collected cancer registry and maternity data in Scotland. METHODS: We conducted a cross-sectional study of 4108 women aged ≤ 50 years with primary breast cancer diagnosed between 2009 and 2016 linked to maternity data. Molecular subtypes of breast cancer were defined using immunohistochemistry (IHC) tumour markers, oestrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2), and tumour grade. Age-adjusted polytomous logistic regression models were used to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association of number of births, age at first birth and time since last birth with IHC-defined breast cancer subtypes. Luminal A-like was the reference compared to luminal B-like (HER2−), luminal B-like (HER2+), HER2-overexpressed and triple-negative breast cancer (TNBC). RESULTS: Mean (SD) for number of births, age at first birth and time since last birth was 1.4 (1.2) births, 27.2 (6.1) years and 11.0 (6.8) years, respectively. Luminal A-like was the most common subtype (40%), while HER2-overexpressed and TNBC represented 5% and 15% of cases, respectively. Larger numbers of births were recorded among women with HER2-overexpressed and TNBC compared with luminal A-like tumours (> 3 vs 0 births, OR 1.87, 95%CI 1.18–2.96; OR 1.44, 95%CI 1.07–1.94, respectively). Women with their most recent birth > 10 years compared to < 2 years were less likely to have TNBC tumours compared to luminal A-like (OR 0.63, 95%CI 0.41–0.97). We found limited evidence for differences by subtype with age at first birth. CONCLUSION: Number of births and time since last birth differed by molecular subtypes of breast cancer among women aged ≤ 50 years. Analyses using linked routine electronic medical records by molecularly defined tumour pathology data can be used to investigate the aetiology and prognosis of cancer

Body Size and Substrate Type Modulate Movement by the Western Pacific Crown-Of-Thorns Starfish, Acanthaster solaris

The movement capacity of the crown-of-thorns starfishes (Acanthaster spp.) is a primary determinant of both their distribution and impact on coral assemblages. We quantified individual movement rates for the Pacific crown-of-thorns starfish (Acanthaster solaris) ranging in size from 75–480 mm total diameter, across three different substrates (sand, flat consolidated pavement, and coral rubble) on the northern Great Barrier Reef. The mean (±SE) rate of movement for smaller (diameter) A. solaris was 23.99 ± 1.02 cm/ min and 33.41 ± 1.49 cm/ min for individuals \u3e350 mm total diameter. Mean (±SE) rates of movement varied with substrate type, being much higher on sand (36.53 ± 1.31 cm/ min) compared to consolidated pavement (28.04 ± 1.15 cm/ min) and slowest across coral rubble (17.25 ± 0.63 cm/ min). If average rates of movement measured here can be sustained, in combination with strong directionality, displacement distances of adult A. solaris could range from 250–520 m/ day, depending on the prevailing substrate. Sustained movement of A. solaris is, however, likely to be highly constrained by habitat heterogeneity, energetic constraints, resource availability, and diurnal patterns of activity, thereby limiting their capacity to move between reefs or habitats

The Changing Face of Water: A Dynamic Reflection of Antibiotic Resistance Across Landscapes

Little is known about the role of surface water in the propagation of antibiotic resistance (AR), or the relationship between AR and water quality declines. While healthcare and agricultural sectors are considered the main contributors to AR dissemination, few studies have been conducted in their absence. Using linear models and Bayesian kriging, we evaluate AR among Escherichia coli water isolates collected bimonthly from the Chobe River in Northern Botswana (n = 1997, n = 414 water samples; July 2011–May 2012) in relation to water quality dynamics (E. coli, fecal coliform, and total suspended solids), land use, season, and AR in wildlife and humans within this system. No commercial agricultural or large medical facilities exist within this region. Here, we identify widespread AR in surface water, with land use and season significant predicators of AR levels. Mean AR was significantly higher in the wet season than the dry season (p = 0.003), and highest in the urban landscape (2.15, SD = 0.098) than the protected landscape (1.39, SD = 0.051). In-water E. coli concentrations were significantly positively associated with mean AR in the wet season (p &lt; 0.001) but not in the dry season (p = 0.110), with TSS negatively associated with mean AR across seasons (p = 0.016 and p = 0.029), identifying temporal and spatial relationships between water quality variables and AR. Importantly, when human, water, and wildlife isolates were examined, similar AR profiles were identified (p &lt; 0.001). Our results suggest that direct human inputs are sufficient for extensive dispersal of AR into the environment, with landscape features, season, and water quality variables influencing AR dynamics. Focused and expensive efforts to minimize pollution from agricultural sources, while important, may only provide incremental benefits to the management of AR across complex landscapes. Controlling direct human AR inputs into the environment remains a critical and pressing challenge

Survey for Transiting Extrasolar Planets in Stellar Systems. II. Spectrophotometry and Metallicities of Open Clusters

We present metallicity estimates for seven open clusters based on spectrophotometric indices from moderate-resolution spectroscopy. Observations of field giants of known metallicity provide a correlation between the spectroscopic indices and the metallicity of open cluster giants. We use \chi^2 analysis to fit the relation of spectrophotometric indices to metallicity in field giants. The resulting function allows an estimate of the target-cluster giants' metallicities with an error in the method of \pm0.08 dex. We derive the following metallicities for the seven open clusters: NGC 1245, [m/H]=-0.14\pm0.04; NGC 2099, [m/H]=+0.05\pm0.05; NGC 2324, [m/H]=-0.06\pm0.04; NGC 2539, [m/H]=-0.04\pm0.03; NGC 2682 (M67), [m/H]=-0.05\pm0.02; NGC 6705, [m/H]=+0.14\pm0.08; NGC 6819, [m/H]=-0.07\pm0.12. These metallicity estimates will be useful in planning future extra-solar planet transit searches since planets may form more readily in metal-rich environments.Comment: 38 pages, including 12 figures. Accepted for publication in A

The thermal emission of the exoplanets WASP-1b and WASP-2b

We present a comparative study of the thermal emission of the transiting exoplanets WASP-1b and WASP-2b using the Spitzer Space Telescope. The two planets have very similar masses but suffer different levels of irradiation and are predicted to fall either side of a sharp transition between planets with and without hot stratospheres. WASP-1b is one of the most highly irradiated planets studied to date. We measure planet/star contrast ratios in all four of the IRAC bands for both planets (3.6-8.0um), and our results indicate the presence of a strong temperature inversion in the atmosphere of WASP-1b, particularly apparent at 8um, and no inversion in WASP-2b. In both cases the measured eclipse depths favor models in which incident energy is not redistributed efficiently from the day side to the night side of the planet. We fit the Spitzer light curves simultaneously with the best available radial velocity curves and transit photometry in order to provide updated measurements of system parameters. We do not find significant eccentricity in the orbit of either planet, suggesting that the inflated radius of WASP-1b is unlikely to be the result of tidal heating. Finally, by plotting ratios of secondary eclipse depths at 8um and 4.5um against irradiation for all available planets, we find evidence for a sharp transition in the emission spectra of hot Jupiters at an irradiation level of 2 x 10^9 erg/s/cm^2. We suggest this transition may be due to the presence of TiO in the upper atmospheres of the most strongly irradiated hot Jupiters.Comment: 10 pages, submitted to Ap

Affordability targets: Implications for Housing Supply

This report presents the results of an econometric modelling project, concerned with regional housing affordability, conducted for the ODPM between November 2004 and April 2005. The key outputs of the project are not just this report, but the model itself, the details of which are set out in the accompanying Technical Appendix, available via the ODPM website: www.odpm.gov.uk/housing. The team for the project was large, including fifteen individuals from nine organisations. The project was directed from the University of Reading. In addition to the team, the work was improved by help from an advisory group and a user group, consisting of members drawn from both central government and from the wider academic and policy communities