Kepler Mission Stellar and Instrument Noise Properties Revisited

An earlier study of the Kepler Mission noise properties on time scales of primary relevance to detection of exoplanet transits found that higher than expected noise followed to a large extent from the stars, rather than instrument or data analysis performance. The earlier study over the first six quarters of Kepler data is extended to the full four years ultimately comprising the mission. Efforts to improve the pipeline data analysis have been successful in reducing noise levels modestly as evidenced by smaller values derived from the current data products. The new analyses of noise properties on transit time scales show significant changes in the component attributed to instrument and data analysis, with essentially no change in the inferred stellar noise. We also extend the analyses to time scales of several days, instead of several hours to better sample stellar noise that follows from magnetic activity. On the longer time scale there is a shift in stellar noise for solar-type stars to smaller values in comparison to solar values.Comment: 10 pages, 8 figures, accepted by A

Phage Display as a Tool for Probing Lipid A Biosynthesis.

The lipid A biosynthetic pathway is exclusive to gram-negative bacteria, thus making it an ideal target for antimicrobial drug discovery. Furthermore, two distinct acyltransferases, UDP-GlcNAc acyltransferase (LpxA) and UDP-3-O-(Acyl)-GlcN acyltransferase (LpxD), display structural and functional similarities within the pathway. Such similarities offer the potential to design inhibitors capable of targeting both active sites. This provides a unique paradigm to combating antimicrobial resistance by decreasing the likelihood that the bacteria would obtain resistance, through increasing the number of mutations necessary for the microbe to survive the therapeutic. Phage display was used to identify several LpxD-inhibitory peptides, one of which (RJPXD33) also inhibited LpxA (LpxD Kd = 7 uM; LpxA Kd = 22 uM) and one which was found to be selective for LpxD (RJPXD34; Kd = 31 uM). Both peptides displayed antimicrobial activity when expressed as N-terminal fusions to thioredoxin. A fluorescence polarization (FP) binding assay was developed for LpxD utilizing a fluorescein-labeled RJPXD33 (Kd = 600 nM) and for LpxA using a fluorescein-labeled Peptide 920 (Kd = 200 nM). With the FP binding assay, RJPXD33 was shown to bind competitively with acyl-ACP. RJPXD33 was co-crystallized with LpxA, in order to gain an understanding of how RJPXD33 binds to LpxA. The structural data suggested that RJPXD33 mimics the acyl-phosphopantetheine moiety of acyl-acyl carrier protein (ACP), the native substrate of LpxA. Biochemical characterization of truncated variations of RJPXD33 confirmed this model and showed that smaller peptides could be synthesized that could inhibit LpxA with similar potency. While RJPXD33 could not be crystallized with LpxD, a crosslinking strategy using photo-affinity derivatives of RJPXD33 was developed for mapping the peptide-protein interactions. Finally, the FP binding assay was employed to screen a small molecule library (~120,000 compounds) against LpxD. The hits were reconfirmed with a continuous, fluorescent enzyme assay developed for both LpxA and LpxD. Eleven compounds ranging in potency (IC50’s = 0.1 - 30 uM) were identified, three of which demonstrated in vivo toxicity in Escherichia coli lacking the multidrug efflux pump, TolC. These molecules provide a foundation for the future development of more potent small molecule inhibitors of LpxD.PHDMedicinal ChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/98051/1/jenkinsr_1.pd

The use of 35S and Tnos expression elements in the measurement of genetically engineered plant materials

An online survey was conducted by the International Life Sciences Institute, Food Biotechnology Committee, on the use of qualitative and quantitative polymerase chain reaction (PCR) assays for cauliflower mosaic virus 35S promoter and Agrobacterium tumefaciens Tnos DNA sequence elements for the detection of genetically engineered (GE) crop plant material. Forty-four testing laboratories around the world completed the survey. The results showed the widespread use of such methods, the multiplicity of published and in-house methods, and the variety of reference materials and calibrants in use. There was an interest on the part of respondents in validated quantitative assays relevant to all GE events that contain these two genetic elements. Data are presented by testing two variations each of five published real-time quantitative PCR methods for 35S detection on eight maize reference materials. The results showed that two of the five methods were not suitable for all the eight reference materials, with poor linear regression parameters and multiple PCR amplification products for some of the reference materials. This study demonstrates that not all 35S methods produce satisfactory results, emphasizing the need for method validation

The Kepler Pixel Response Function

Kepler seeks to detect sequences of transits of Earth-size exoplanets orbiting Solar-like stars. Such transit signals are on the order of 100 ppm. The high photometric precision demanded by Kepler requires detailed knowledge of how the Kepler pixels respond to starlight during a nominal observation. This information is provided by the Kepler pixel response function (PRF), defined as the composite of Kepler's optical point spread function, integrated spacecraft pointing jitter during a nominal cadence and other systematic effects. To provide sub-pixel resolution, the PRF is represented as a piecewise-continuous polynomial on a sub-pixel mesh. This continuous representation allows the prediction of a star's flux value on any pixel given the star's pixel position. The advantages and difficulties of this polynomial representation are discussed, including characterization of spatial variation in the PRF and the smoothing of discontinuities between sub-pixel polynomial patches. On-orbit super-resolution measurements of the PRF across the Kepler field of view are described. Two uses of the PRF are presented: the selection of pixels for each star that maximizes the photometric signal to noise ratio for that star, and PRF-fitted centroids which provide robust and accurate stellar positions on the CCD, primarily used for attitude and plate scale tracking. Good knowledge of the PRF has been a critical component for the successful collection of high-precision photometry by Kepler.Comment: 10 pages, 5 figures, accepted by ApJ Letters. Version accepted for publication

Initial Characteristics of Kepler Short Cadence Data

The Kepler Mission offers two options for observations -- either Long Cadence (LC) used for the bulk of core mission science, or Short Cadence (SC) which is used for applications such as asteroseismology of solar-like stars and transit timing measurements of exoplanets where the 1-minute sampling is critical. We discuss the characteristics of SC data obtained in the 33.5-day long Quarter 1 (Q1) observations with Kepler which completed on 15 June 2009. The truly excellent time series precisions are nearly Poisson limited at 11th magnitude providing per-point measurement errors of 200 parts-per-million per minute. For extremely saturated stars near 7th magnitude precisions of 40 ppm are reached, while for background limited measurements at 17th magnitude precisions of 7 mmag are maintained. We note the presence of two additive artifacts, one that generates regularly spaced peaks in frequency, and one that involves additive offsets in the time domain inversely proportional to stellar brightness. The difference between LC and SC sampling is illustrated for transit observations of TrES-2.Comment: 5 pages, 4 figures, ApJ Letters in pres

Photometric Variability in Kepler Target Stars: The Sun Among Stars -- A First Look

The Kepler mission provides an exciting opportunity to study the lightcurves of stars with unprecedented precision and continuity of coverage. This is the first look at a large sample of stars with photometric data of a quality that has heretofore been only available for our Sun. It provides the first opportunity to compare the irradiance variations of our Sun to a large cohort of stars ranging from vary similar to rather different stellar properties, at a wide variety of ages. Although Kepler data is in an early phase of maturity, and we only analyze the first month of coverage, it is sufficient to garner the first meaningful measurements of our Sun's variability in the context of a large cohort of main sequence stars in the solar neighborhood. We find that nearly half of the full sample is more active than the active Sun, although most of them are not more than twice as active. The active fraction is closer to a third for the stars most similar to the Sun, and rises to well more than half for stars cooler than mid K spectral types.Comment: 13 pages, 4 figures, accepted to ApJ Letter

Kepler Mission Stellar and Instrument Noise Properties

Kepler Mission results are rapidly contributing to fundamentally new discoveries in both the exoplanet and asteroseismology fields. The data returned from Kepler are unique in terms of the number of stars observed, precision of photometry for time series observations, and the temporal extent of high duty cycle observations. As the first mission to provide extensive time series measurements on thousands of stars over months to years at a level hitherto possible only for the Sun, the results from Kepler will vastly increase our knowledge of stellar variability for quiet solar-type stars. Here we report on the stellar noise inferred on the timescale of a few hours of most interest for detection of exoplanets via transits. By design the data from moderately bright Kepler stars are expected to have roughly comparable levels of noise intrinsic to the stars and arising from a combination of fundamental limitations such as Poisson statistics and any instrument noise. The noise levels attained by Kepler on-orbit exceed by some 50% the target levels for solar-type, quiet stars. We provide a decomposition of observed noise for an ensemble of 12th magnitude stars arising from fundamental terms (Poisson and readout noise), added noise due to the instrument and that intrinsic to the stars. The largest factor in the modestly higher than anticipated noise follows from intrinsic stellar noise. We show that using stellar parameters from galactic stellar synthesis models, and projections to stellar rotation, activity and hence noise levels reproduces the primary intrinsic stellar noise features.Comment: Accepted by ApJ; 26 pages, 20 figure