Using Exploratory Data Analytics to Identify Deficiencies in mCherry Red Fluorescent Protein and Suggest Improvements

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An Improved Cerulean Fluorescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching

Cyan fluorescent proteins (CFPs), such as Cerulean, are widely used as donor fluorophores in Förster resonance energy transfer (FRET) experiments. Nonetheless, the most widely used variants suffer from drawbacks that include low quantum yields and unstable flurorescence. To improve the fluorescence properties of Cerulean, we used the X-ray structure to rationally target specific amino acids for optimization by site-directed mutagenesis. Optimization of residues in strands 7 and 8 of the β-barrel improved the quantum yield of Cerulean from 0.48 to 0.60. Further optimization by incorporating the wild-type T65S mutation in the chromophore improved the quantum yield to 0.87. This variant, mCerulean3, is 20% brighter and shows greatly reduced fluorescence photoswitching behavior compared to the recently described mTurquoise fluorescent protein in vitro and in living cells. The fluorescence lifetime of mCerulean3 also fits to a single exponential time constant, making mCerulean3 a suitable choice for fluorescence lifetime microscopy experiments. Furthermore, inclusion of mCerulean3 in a fusion protein with mVenus produced FRET ratios with less variance than mTurquoise-containing fusions in living cells. Thus, mCerulean3 is a bright, photostable cyan fluorescent protein which possesses several characteristics that are highly desirable for FRET experiments

Gemini GMOS and WHT SAURON integral-field spectrograph observations of the AGN driven outflow in NGC 1266

We use the SAURON and GMOS integral field spectrographs to observe the active galactic nucleus (AGN) powered outflow in NGC 1266. This unusual galaxy is relatively nearby (D=30 Mpc), allowing us to investigate the process of AGN feedback in action. We present maps of the kinematics and line strengths of the ionised gas emission lines Halpha, Hbeta, [OIII], [OI], [NII] and [SII], and report on the detection of Sodium D absorption. We use these tracers to explore the structure of the source, derive the ionised and atomic gas kinematics and investigate the gas excitation and physical conditions. NGC 1266 contains two ionised gas components along most lines of sight, tracing the ongoing outflow and a component closer to the galaxy systemic, the origin of which is unclear. This gas appears to be disturbed by a nascent AGN jet. We confirm that the outflow in NGC 1266 is truly multiphase, containing radio plasma, atomic, molecular and ionised gas and X-ray emitting plasma. The outflow has velocities up to \pm900 km/s away from the systemic velocity, and is very likely to be removing significant amounts of cold gas from the galaxy. The LINER-like line-emission in NGC 1266 is extended, and likely arises from fast shocks caused by the interaction of the radio jet with the ISM. These shocks have velocities of up to 800 km/s, which match well with the observed velocity of the outflow. Sodium D equivalent width profiles are used to set constraints on the size and orientation of the outflow. The ionised gas morphology correlates with the nascent radio jets observed in 1.4 GHz and 5 GHz continuum emission, supporting the suggestion that an AGN jet is providing the energy required to drive the outflow.Comment: Contains 18 figures. Accepted to MNRA

The ATLAS(3D) project - II. Morphologies, kinemetric features and alignment between photometric and kinematic axes of early-type galaxies

The definitive version can be found at: http://onlinelibrary.wiley.com/ Copyright Royal Astronomical SocietyWe use the ATLAS(3D) sample of 260 early-type galaxies to study the apparent kinematic misalignment angle, Psi, defined as the angle between the photometric and kinematic major axes. We find that 71 per cent of nearby early-type galaxies are strictly aligned systems (Psi <= 5 degrees), an additional 14 per cent have 5 degrees < Psi < 10 degrees and 90 per cent of galaxies have Psi <= 15 degrees. Taking into account measurement uncertainties, 90 per cent of galaxies can be considered aligned to better than 5 degrees, suggesting that only a small fraction of early-type galaxies (similar to 10 per cent) are not consistent with the axisymmetry within the projected half-light radius. We identify morphological features such as bars and rings (30 per cent), dust structures (16 per cent), blue nuclear colours (6 per cent) and evidence of interactions (8 per cent) visible on ATLAS(3D) galaxies. We use KINEMETRY to analyse the mean velocity maps and separate galaxies into two broad types of regular and non-regular rotators. We find 82 per cent of regular rotators and 17 per cent of non-regular rotators, with two galaxies that we were not able to classify due to the poor data quality. The non-regular rotators are typically found in dense regions and are massive. We characterize the specific features in the mean velocity and velocity dispersion maps. The majority of galaxies do not have any specific features, but we highlight here the frequency of the kinematically distinct cores (7 per cent of galaxies) and the aligned double peaks in the velocity dispersion maps (4 per cent of galaxies). We separate galaxies into five kinematic groups based on the kinemetric features, which are then used to interpret the (Psi-epsilon) diagram. Most of the galaxies that are misaligned have complex kinematics and are non-regular rotators. In addition, some show evidence of the interaction and might not be in equilibrium, while some are barred. While the trends are weak, there is a tendency that large values of Psi are found in galaxies at intermediate environmental densities and among the most massive galaxies in the sample. Taking into account the kinematic alignment and the kinemetric analysis, the majority of early-type galaxies have velocity maps more similar to that of the spiral discs than to that of the remnants of equal-mass mergers. We suggest that the most common formation mechanism for early-type galaxies preserves the axisymmetry of the disc progenitors and their general kinematic properties. Less commonly, the formation process results in a triaxial galaxy with much lower net angular momentum.Peer reviewe