Targeted rapid amplification of cDNA ends (T-RACE)—an improved RACE reaction through degradation of non-target sequences

Amplification of the 5′ ends of cDNA, although simple in theory, can often be difficult to achieve. We describe a novel method for the specific amplification of cDNA ends. An oligo-dT adapter incorporating a dUTP-containing PCR primer primes first-strand cDNA synthesis incorporating dUTP. Using the Cap finder approach, another distinct dUTP containing adapter is added to the 3′ end of the newly synthesized cDNA. Second-strand synthesis incorporating dUTP is achieved by PCR, using dUTP-containing primers complimentary to the adapter sequences incorporated in the cDNA ends. The double-stranded cDNA-containing dUTP serves as a universal template for the specific amplification of the 3′ or 5′ end of any gene. To amplify the ends of cDNA, asymmetric PCR is performed using a single gene-specific primer and standard dNTPs. The asymmetric PCR product is purified and non-target transcripts containing dUTP degraded by Uracil DNA glycosylase, leaving only those transcripts produced during the asymmetric PCR. Subsequent PCR using a nested gene-specific primer and the 3′ or 5′ T-RACE primer results in specific amplification of cDNA ends. This method can be used to specifically amplify the 3′ and 5′ ends of numerous cDNAs from a single cDNA synthesis reaction

On the Gravitomagnetic Time Delay

We study the gravitational time delay in ray propagation due to rotating masses in the linear approximation of general relativity. Simple expressions are given for the gravitomagnetic time delay that occurs when rays of radiation cross a slowly rotating shell and propagate in the field of a distant rotating source. Moreover, we calculate the local gravitational time delay in the Goedel universe. The observational consequences of these results in the case of weak gravitational lensing are discussed.Comment: 15 pages, 1 figure, revised version submitted to Phys. Lett.

Multi-band optical micro-variability observations of BL Lacertae

We have observed BL Lacertae in the B, R and I bands for 2 nights in July, 1999, and 3 nights in July, 2001. The observations resulted in almost evenly sampled light curves, with an average sampling interval of ~5 min. The source is significantly variable in all bands. On average, the variability amplitude increases from ~5% in the I band, to ~5.5% in the R and ~6.5% in the B band light curves. The rising and decaying time scales are comparable within each band, but they increase from the B, to R and I band light curves. The optical power spectrum shows a red noise component with a slope of ~ -2. Cross-correlation analysis shows that in most cases the delay between the variations in the B and I band light curves is less than ~ 0.4 hrs. The cross-correlation functions are asymmetric, implying complex delays of the I band variations with respect to the B band variations. Furthermore, in one case we find that the I band variations are significantly delayed (by ~0.2 hrs) with respect to the B band variations. We also detect significant spectral variations: the spectrum becomes steeper as the flux increases, and the flattest spectral index corresponds to the maximum B band flux. Our results imply that the fast, intra-night variations of the source correspond to perturbations of different regions in the jet which cause localized injections of relativistic particles on time scales much sorter that the average sampling interval of the light curves. The variations are controlled by the cooling and light crossing time scales, which are probably comparable.Comment: Accepted for publication in A&

Canonical formulation of self-gravitating spinning-object systems

Based on the Arnowitt-Deser-Misner (ADM) canonical formulation of general relativity, a canonical formulation of gravitationally interacting classical spinning-object systems is given to linear order in spin. The constructed position, linear momentum and spin variables fulfill standard Poisson bracket relations. A spatially symmetric time gauge for the tetrad field is introduced. The achieved formulation is of fully reduced form without unresolved constraints, supplementary, gauge, or coordinate conditions. The canonical field momentum is not related to the extrinsic curvature of spacelike hypersurfaces in standard ADM form. A new reduction of the tetrad degrees of freedom to the Einstein form of the metric field is suggested.Comment: 6 pages. v2: extended version; identical to the published one. v3: corrected misprints in (24) and (39); improved notation; added note regarding a further reference

The Shortest Period Detached Binary White Dwarf System

We identify SDSS J010657.39-100003.3 (hereafter J0106-1000) as the shortest period detached binary white dwarf (WD) system currently known. We targeted J0106-1000 as part of our radial velocity program to search for companions around known extremely low-mass (ELM, ~ 0.2 Msol) WDs using the 6.5m MMT. We detect peak-to-peak radial velocity variations of 740 km/s with an orbital period of 39.1 min. The mass function and optical photometry rule out a main-sequence star companion. Follow-up high-speed photometric observations obtained at the McDonald 2.1m telescope reveal ellipsoidal variations from the distorted primary but no eclipses. This is the first example of a tidally distorted WD. Modeling the lightcurve, we constrain the inclination angle of the system to be 67 +- 13 deg. J0106-1000 contains a pair of WDs (0.17 Msol primary + 0.43 Msol invisible secondary) at a separation of 0.32 Rsol. The two WDs will merge in 37 Myr and most likely form a core He-burning single subdwarf star. J0106-1000 is the shortest timescale merger system currently known. The gravitational wave strain from J0106-1000 is at the detection limit of the Laser Interferometer Space Antenna (LISA). However, accurate ephemeris and orbital period measurements may enable LISA to detect J0106-1000 above the Galactic background noise.Comment: MNRAS Letters, in pres

Photometric characterization of exoplanets using angular and spectral differential imaging

The direct detection of exoplanets has been the subject of intensive research in the recent years. Data obtained with future high-contrast imaging instruments optimized for giant planets direct detection are strongly limited by the speckle noise. Specific observing strategies and data analysis methods, such as angular and spectral differential imaging, are required to attenuate the noise level and possibly detect the faint planet flux. Even though these methods are very efficient at suppressing the speckles, the photometry of the faint planets is dominated by the speckle residuals. The determination of the effective temperature and surface gravity of the detected planets from photometric measurements in different bands is then limited by the photometric error on the planet flux. In this work we investigate this photometric error and the consequences on the determination of the physical parameters of the detected planets. We perform detailed end-to-end simulation with the CAOS-based Software Package for SPHERE to obtain realistic data representing typical observing sequences in Y, J, H and Ks bands with a high contrast imager. The simulated data are used to measure the photometric accuracy as a function of contrast for planets detected with angular and spectral+angular differential methods. We apply this empirical accuracy to study the characterization capabilities of a high-contrast differential imager. We show that the expected photometric performances will allow the detection and characterization of exoplanets down to the Jupiter mass at angular separations of 1.0" and 0.2" respectively around high mass and low mass stars with 2 observations in different filter pairs. We also show that the determination of the planets physical parameters from photometric measurements in different filter pairs is essentialy limited by the error on the determination of the surface gravity.Comment: 13 pages, 7 figures, 4 tables. Accepted for publication in MNRA

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

The idea of 'date' and 'party' hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. Thus, we suggest that a date/party dichotomy is not meaningful and it might be more useful to conceive of roles for protein-protein interactions rather than individual proteins. We find significant correlations between interaction centrality and the functional similarity of the interacting proteins.Comment: 27 pages, 5 main figures, 4 supplementary figure

Disagreements with implications: diverging discourses on the ethics of non-medical use of methylphenidate for performance enhancement

<p>Abstract</p> <p>Background</p> <p>There is substantial evidence that methylphenidate (MPH; Ritalin), is being used by healthy university students for non-medical motives such as the improvement of concentration, alertness, and academic performance. The scope and potential consequences of the non-medical use of MPH upon healthcare and society bring about many points of view.</p> <p>Methods</p> <p>To gain insight into key ethical and social issues on the non-medical use of MPH, we examined discourses in the print media, bioethics literature, and public health literature.</p> <p>Results</p> <p>Our study identified three diverging paradigms with varying perspectives on the nature of performance enhancement. The beneficial effects of MPH on normal cognition were generally portrayed enthusiastically in the print media and bioethics discourses but supported by scant information on associated risks. Overall, we found a variety of perspectives regarding ethical, legal and social issues related to the non-medical use of MPH for performance enhancement and its impact upon social practices and institutions. The exception to this was public health discourse which took a strong stance against the non-medical use of MPH typically viewed as a form of prescription abuse or misuse. Wide-ranging recommendations for prevention of further non-medical use of MPH included legislation and increased public education.</p> <p>Conclusion</p> <p>Some positive portrayals of the non-medical use of MPH for performance enhancement in the print media and bioethics discourses could entice further uses. Medicine and society need to prepare for more prevalent non-medical uses of neuropharmaceuticals by fostering better informed public debates.</p

NACO Polarimetric Differential Imaging of TW Hya: A Sharp Look at the Closest T Tauri Disk

We present high-contrast imaging data on the disk of the classical T Tauri star TW Hya. The images were obtained through the polarimetric differential imaging technique with the adaptive optics system NACO. Our commissioning data show the presence of polarized disk emission between 0.1" and 1.4" from the star. We derive the first Ks-band radial polarized intensity distribution. We show that the polarized intensity compares well to shorter wavelengths surface brightness observations and confirm the previously reported gradual slope change around 0.8". These results show the potential of the new polarimetric differential imaging technique at 8m-class telescopes to map the inner regions of protoplanetary disks.Comment: Accepted for publication in Astronomy & Astrophysics; 7 pages, 7 figure

Dark energy with gravitational lens time delays

Strong lensing gravitational time delays are a powerful and cost effective probe of dark energy. Recent studies have shown that a single lens can provide a distance measurement with 6-7 % accuracy (including random and systematic uncertainties), provided sufficient data are available to determine the time delay and reconstruct the gravitational potential of the deflector. Gravitational-time delays are a low redshift (z~0-2) probe and thus allow one to break degeneracies in the interpretation of data from higher-redshift probes like the cosmic microwave background in terms of the dark energy equation of state. Current studies are limited by the size of the sample of known lensed quasars, but this situation is about to change. Even in this decade, wide field imaging surveys are likely to discover thousands of lensed quasars, enabling the targeted study of ~100 of these systems and resulting in substantial gains in the dark energy figure of merit. In the next decade, a further order of magnitude improvement will be possible with the 10000 systems expected to be detected and measured with LSST and Euclid. To fully exploit these gains, we identify three priorities. First, support for the development of software required for the analysis of the data. Second, in this decade, small robotic telescopes (1-4m in diameter) dedicated to monitoring of lensed quasars will transform the field by delivering accurate time delays for ~100 systems. Third, in the 2020's, LSST will deliver 1000's of time delays; the bottleneck will instead be the aquisition and analysis of high resolution imaging follow-up. Thus, the top priority for the next decade is to support fast high resolution imaging capabilities, such as those enabled by the James Webb Space Telescope and next generation adaptive optics systems on large ground based telescopes.Comment: White paper submitted to SNOWMASS201