302 research outputs found
A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
Detection of DNA methylation in the genome has been possible for decades; however, the ability to deliberately and specifically manipulate local DNA methylation states in the genome has been extremely limited. Consequently, this has impeded our understanding of the direct effect of DNA methylation on transcriptional regulation and transcription factor binding in the native chromatin context. Thus, highly specific targeted epigenome editing tools are needed to address this. Recent adaptations of genome editing technologies, including fusion of the DNMT3A DNA methyltransferase catalytic domain to catalytically inactive Cas9 (dC9-D3A), have aimed to alter DNA methylation at desired loci. Here, we show that these tools exhibit consistent off-target DNA methylation deposition in the genome, limiting their capabilities to unambiguously assess the functional consequences of DNA methylation. To address this, we developed a modular dCas9-SunTag (dC9Sun-D3A) system that can recruit multiple DNMT3A catalytic domains to a target site for editing DNA methylation. dC9Sun-D3A is tunable, specific, and exhibits much higher induction of DNA methylation at target sites than the dC9-D3A direct fusion protein. Importantly, genome-wide characterization of dC9Sun-D3A binding sites and DNA methylation revealed minimal off-target protein binding and induction of DNA methylation with dC9Sun-D3A, compared to pervasive off-target methylation by dC9-D3A. Furthermore, we used dC9Sun-D3A to demonstrate the binding sensitivity to DNA methylation for CTCF and NRF1 in situ. Overall, this modular dC9Sun-D3A system enables precise DNA methylation deposition with the lowest off-target DNA methylation levels reported to date, allowing accurate functional determination of the role of DNA methylation at single loci.Christian Pflueger, Dennis Tan, Tessa Swain, Trung Nguyen, Jahnvi Pflueger, Christian Nefzger ... et al
WASP-23b: a transiting hot Jupiter around a K dwarf and its Rossiter-McLaughlin effect
We report the discovery of a new transiting planet in the Southern
Hemisphere. It has been found by the WASP-south transit survey and confirmed
photometrically and spectroscopically by the 1.2m Swiss Euler telescope, LCOGT
2m Faulkes South Telescope, the 60 cm TRAPPIST telescope and the ESO 3.6m
telescope. The orbital period of the planet is 2.94 days. We find it is a gas
giant with a mass of 0.88 \pm 0.10 Mj and a radius estimated at 0.96 \pm 0.05
Rj . We have also obtained spectra during transit with the HARPS spectrograph
and detect the Rossiter-McLaughlin effect despite its small amplitude. Because
of the low signal to noise of the effect and of a small impact parameter we
cannot place a constraint on the projected spin-orbit angle. We find two
confiicting values for the stellar rotation. Our determination, via spectral
line broadening gives v sin I = 2.2 \pm 0.3 km/s, while another method, based
on the activity level using the index log R'HK, gives an equatorial rotation
velocity of only v = 1.35 \pm 0.20 km/s. Using these as priors in our analysis,
the planet could either be misaligned or aligned. This should send strong
warnings regarding the use of such priors. There is no evidence for
eccentricity nor of any radial velocity drift with time.Comment: 13 pages, 8 figures, 7 tables, accepted for publication in A&
Discovery and characterization of WASP-6b, an inflated sub-Jupiter mass planet transiting a solar-type star
We report the discovery of WASP-6b, an inflated sub-Jupiter mass planet transiting every 3.3610060^{\rm + 0.0000022 }_ days a mildly metal-poor solar-type star of magnitude V = 11.9. A combined analysis of the WASP photometry, high-precision followup transit photometry and radial velocities yield a planetary mass M_{\rm p} = 0.503^_ and radius R_{\rm p} = 1.224^_ , resulting in a density . The mass and radius for the host star are M_\ast = 0.88^_ and R_\ast = 0.870^_ . The non-zero orbital eccentricity e = 0.054^{\rm +0.018}_ that we measure suggests that the planet underwent a massive tidal heating ~1 Gyr ago that could have contributed to its inflated radius. High-precision radial velocities obtained during a transit allow us to measure a sky-projected angle between the stellar spin and orbital axis \beta = 11^_ deg. In addition to similar published measurements, this result favors a dominant migration mechanism based on tidal interactions with a protoplanetary disk
WASP-42 b and WASP-49 b: two new transiting sub-Jupiters
We report the discovery of two new transiting planets from the WASP survey.
WASP-42 b is a 0.500 +/- 0.035 M_jup planet orbiting a K1 star at a separation
of 0.0548 +/- 0.0017 AU with a period of 4.9816872 +/- 7.3 x 10^-6 days. The
radius of WASP-42 b is 1.080 +/- 0.057 R_jup while its equilibrium temperature
is T_eq = 995 +/- 34 K. We detect some evidence for a small but non-zero
eccentricity of e=0.060 +/- 0.013. WASP-49 b is a 0.378 +/- 0.027 M_jup planet
around an old G6 star. It has a period of 2.7817387 +/- 5.6 x 10^-6 days and a
separation of 0.0379 +/- 0.0011 AU. This planet is slightly bloated, having a
radius of 1.115 +/- 0.047 R_jup and an equilibrium temperature of T_eq = 1369
+/- 39 K. Both planets have been followed up photometrically, and in total we
have obtained 5 full and one partial transit light curves of WASP-42 and 4 full
and one partial light curves of WASP-49 using the Euler-Swiss, TRAPPIST and
Faulkes South telescopes
Rossiter-McLaughlin Effect Measurements for WASP-16, WASP-25 and WASP-31
We present new measurements of the Rossiter-McLaughlin (RM) effect for three
WASP planetary systems, WASP-16, WASP-25 and WASP-31, from a combined analysis
of their complete sets of photometric and spectroscopic data. We find a low
amplitude RM effect for WASP-16 (Teff = 5700 \pm 150K), suggesting that the
star is a slow rotator and thus of an advanced age, and obtain a projected
alignment angle of lambda = -4.2 degrees +11.0 -13.9. For WASP-25 (Teff =
5750\pm100K) we detect a projected spin-orbit angle of lambda = 14.6 degrees
\pm6.7. WASP-31 (Teff = 6300\pm100K) is found to be well-aligned, with a
projected spin-orbit angle of lambda = 2.8degrees \pm3.1. A circular orbit is
consistent with the data for all three systems, in agreement with their
respective discovery papers. We consider the results for these systems in the
context of the ensemble of RM measurements made to date. We find that whilst
WASP-16 fits the hypothesis of Winn et al. (2010) that 'cool' stars (Teff <
6250K) are preferentially aligned, WASP-31 has little impact on the proposed
trend. We bring the total distribution of the true spin-orbit alignment angle,
psi, up to date, noting that recent results have improved the agreement with
the theory of Fabrycky & Tremaine (2007) at mid-range angles. We also suggest a
new test for judging misalignment using the Bayesian Information Criterion,
according to which WASP-25 b's orbit should be considered to be aligned.Comment: 20 pages, 14 tables, 10 figures. Accepted to MNRA
Measurement of the Forward-Backward Asymmetry in the B -> K(*) mu+ mu- Decay and First Observation of the Bs -> phi mu+ mu- Decay
We reconstruct the rare decays , , and in a data sample
corresponding to collected in collisions at
by the CDF II detector at the Fermilab Tevatron
Collider. Using and decays we report the branching ratios. In addition, we report
the measurement of the differential branching ratio and the muon
forward-backward asymmetry in the and decay modes, and the
longitudinal polarization in the decay mode with respect to the squared
dimuon mass. These are consistent with the theoretical prediction from the
standard model, and most recent determinations from other experiments and of
comparable accuracy. We also report the first observation of the {\mathcal{B}}(B^0_s \to
\phi\mu^+\mu^-) = [1.44 \pm 0.33 \pm 0.46] \times 10^{-6}27 \pm 6B^0_s$ decay observed.Comment: 7 pages, 2 figures, 3 tables. Submitted to Phys. Rev. Let
Measurements of the properties of Lambda_c(2595), Lambda_c(2625), Sigma_c(2455), and Sigma_c(2520) baryons
We report measurements of the resonance properties of Lambda_c(2595)+ and
Lambda_c(2625)+ baryons in their decays to Lambda_c+ pi+ pi- as well as
Sigma_c(2455)++,0 and Sigma_c(2520)++,0 baryons in their decays to Lambda_c+
pi+/- final states. These measurements are performed using data corresponding
to 5.2/fb of integrated luminosity from ppbar collisions at sqrt(s) = 1.96 TeV,
collected with the CDF II detector at the Fermilab Tevatron. Exploiting the
largest available charmed baryon sample, we measure masses and decay widths
with uncertainties comparable to the world averages for Sigma_c states, and
significantly smaller uncertainties than the world averages for excited
Lambda_c+ states.Comment: added one reference and one table, changed order of figures, 17
pages, 15 figure
Search for a New Heavy Gauge Boson Wprime with Electron + missing ET Event Signature in ppbar collisions at sqrt(s)=1.96 TeV
We present a search for a new heavy charged vector boson decaying
to an electron-neutrino pair in collisions at a center-of-mass
energy of 1.96\unit{TeV}. The data were collected with the CDF II detector
and correspond to an integrated luminosity of 5.3\unit{fb}^{-1}. No
significant excess above the standard model expectation is observed and we set
upper limits on . Assuming standard
model couplings to fermions and the neutrino from the boson decay to
be light, we exclude a boson with mass less than
1.12\unit{TeV/}c^2 at the 95\unit{%} confidence level.Comment: 7 pages, 2 figures Submitted to PR
Performance of the CMS Cathode Strip Chambers with Cosmic Rays
The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device
in the CMS endcaps. Their performance has been evaluated using data taken
during a cosmic ray run in fall 2008. Measured noise levels are low, with the
number of noisy channels well below 1%. Coordinate resolution was measured for
all types of chambers, and fall in the range 47 microns to 243 microns. The
efficiencies for local charged track triggers, for hit and for segments
reconstruction were measured, and are above 99%. The timing resolution per
layer is approximately 5 ns
An Early-Time Infrared and Optical Study of the Type Ia Supernova 1998bu in M96
We present first-season infrared (IR) and optical photometry and spectroscopy
of the Type Ia Supernova 1998bu in M96. We also report optical polarimetry of
this event. SN1998bu is one of the closest type Ia Supernovae of modern times
and the distance of its host galaxy is well-determined. We find that SN1998bu
is both photometrically and spectroscopically normal. However, the extinction
to this event is unusually high, with Av=1.0 +/-0.11. We find that SN1998bu
peaked at an intrinsic Mv=-19.37 +/-0.23. Adopting a distance modulus of 30.25
(Tanvir et al. 1999) and using Phillips et al.'s (1999) relations for the
Hubble constant we obtain Ho=70.4 +/-4.3 km/s/Mpc. Combination of our IR
photometry with those of Jha et al. (1999) provides one of the most complete
early-phase IR light curves for a SN Ia published so far. In particular, SN
1998bu is the first normal SN Ia for which good pre-maximum (in the B band) IR
coverage has been obtained. It reveals that the J, H and K light curves peak
about 5 days earlier than the flux in the B-band curve.Comment: 22 pages, 9 figues, accepted for publication by MNRA
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