Noncoding RNAs and gene silencing

Noncoding RNA has long been proposed to control gene expression via sequence-specific interactions with regulatory regions. Here, we review the role of noncoding RNA in heterochromatic silencing and in the silencing of transposable elements (TEs), unpaired DNA in meiosis, and developmentally excised DNA. The role of cotranscriptional processing by RNA interference and by other mechanisms is discussed, as well as parallels with RNA silencing in imprinting, paramutation, polycomb silencing, and X inactivation. Interactions with regulatory sequences may well occur, but at the RNA rather than at the DNA level

Crossing the `Yellow Void' -- Spatially Resolved Spectroscopy of the Post- Red Supergiant IRC+10420 and Its Circumstellar Ejecta

IRC +10420 is one of the extreme hypergiant stars that define the empirical upper luminosity boundary in the HR diagram. During their post--RSG evolution, these massive stars enter a temperature range (6000-9000 K) of increased dynamical instability, high mass loss, and increasing opacity, a semi--forbidden region, that de Jager and his collaborators have called the `yellow void'. We report HST/STIS spatially resolved spectroscopy of IRC +10420 and its reflection nebula with some surprising results. Long slit spectroscopy of the reflected spectrum allows us to effectively view the star from different directions. Measurements of the double--peaked Halpha emission profile show a uniform outflow of gas in a nearly spherical distribution, contrary to previous models with an equatorial disk or bipolar outflow. Based on the temperature and mass loss rate estimates that are usually quoted for this object, the wind is optically thick to the continuum at some and possibly all wavelengths. Consequently the observed variations in apparent spectral type and inferred temperature are changes in the wind and do not necessarily mean that the underlying stellar radius and interior structure are evolving on such a short timescale. To explain the evidence for simultaneous outflow and infall of material near the star, we propose a `rain' model in which blobs of gas condense in regions of lowered opacity outside the dense wind. With the apparent warming of its wind, the recent appearance of strong emission, and a decline in the mass loss rate, IRC +10420 may be about to shed its opaque wind, cross the `yellow void', and emerge as a hotter star.Comment: To appear in the Astronomical Journal, August 200

Albedo and Reflection Spectra of Extrasolar Giant Planets

We generate theoretical albedo and reflection spectra for a full range of extrasolar giant planet (EGP) models, from Jovian to 51-Pegasi class objects. Our albedo modeling utilizes the latest atomic and molecular cross sections, a Mie theory treatment of extinction by condensates, a variety of particle size distributions, and an extension of the Feautrier radiative transfer method which allows for a general treatment of the scattering phase function. We find that due to qualitative similarities in the compositions and spectra of objects within each of five broad effective temperature ranges, it is natural to establish five representative EGP albedo classes: a ``Jovian'' class (T$_{\rm eff} \lesssim 150$ K; Class I) with tropospheric ammonia clouds, a ``water cloud'' class (T$_{\rm eff} \sim 250$ K; Class II) primarily affected by condensed H$_2$O, a ``clear'' class (T$_{\rm eff} \gtrsim 350$ K; Class III) which lacks clouds, and two high-temperature classes: Class IV (900 K $\lesssim$ T$_{\rm{eff}}$ $\lesssim$ 1500 K) for which alkali metal absorption predominates, and Class V (T$_{\rm{eff}}$ $\gtrsim$ 1500 K and/or low surface gravity ($\lesssim$ 10$^3$ cm s$^{-2}$)) for which a high silicate layer shields a significant fraction of the incident radiation from alkali metal and molecular absorption. The resonance lines of sodium and potassium are expected to be salient features in the reflection spectra of Class III, IV, and V objects. We derive Bond albedos and effective temperatures for the full set of known EGPs and explore the possible effects of non-equilibrium condensed products of photolysis above or within principal cloud decks. As in Jupiter, such species can lower the UV/blue albedo substantially, even if present in relatively small mixing ratios.Comment: revised LaTeX manuscript accepted to Ap.J.; also available at http://jupiter.as.arizona.edu/~burrows/paper

The influence of the cosmological expansion on local systems

Following renewed interest, the problem of whether the cosmological expansion affects the dynamics of local systems is reconsidered. The cosmological correction to the equations of motion in the locally inertial Fermi normal frame (the relevant frame for astronomical observations) is computed. The evolution equations for the cosmological perturbation of the two--body problem are solved in this frame. The effect on the orbit is insignificant as are the effects on the galactic and galactic--cluster scales.Comment: To appear in the Astrophysical Journal, Late

Susceptibility of hamsters to clostridium difficile isolates of differing toxinotype

Clostridium difficile is the most commonly associated cause of antibiotic associated disease (AAD), which caused ~21,000 cases of AAD in 2011 in the U.K. alone. The golden Syrian hamster model of CDI is an acute model displaying many of the clinical features of C. difficile disease. Using this model we characterised three clinical strains of C. difficile, all differing in toxinotype; CD1342 (PaLoc negative), M68 (toxinotype VIII) and BI-7 (toxinotype III). The naturally occurring non-toxic strain colonised all hamsters within 1-day post challenge (d.p.c.) with high-levels of spores being shed in the faeces of animals that appeared well throughout the entire experiment. However, some changes including increased neutrophil influx and unclotted red blood cells were observed at early time points despite the fact that the known C. difficile toxins (TcdA, TcdB and CDT) are absent from the genome. In contrast, hamsters challenged with strain M68 resulted in a 45% mortality rate, with those that survived challenge remaining highly colonised. It is currently unclear why some hamsters survive infection, as bacterial and toxin levels and histology scores were similar to those culled at a similar time-point. Hamsters challenged with strain BI-7 resulted in a rapid fatal infection in 100% of the hamsters approximately 26 hr post challenge. Severe caecal pathology, including transmural neutrophil infiltrates and extensive submucosal damage correlated with high levels of toxin measured in gut filtrates ex vivo. These data describes the infection kinetics and disease outcomes of 3 clinical C. difficile isolates differing in toxin carriage and provides additional insights to the role of each toxin in disease progression

Asexuality: Classification and characterization

This is a post-print version of the article. The official published version can be obtaineed at the link below.The term “asexual” has been defined in many different ways and asexuality has received very little research attention. In a small qualitative study (N = 4), individuals who self-identified as asexual were interviewed to help formulate hypotheses for a larger study. The second larger study was an online survey drawn from a convenience sample designed to better characterize asexuality and to test predictors of asexual identity. A convenience sample of 1,146 individuals (N = 41 self-identified asexual) completed online questionnaires assessing sexual history, sexual inhibition and excitation, sexual desire, and an open-response questionnaire concerning asexual identity. Asexuals reported significantly less desire for sex with a partner, lower sexual arousability, and lower sexual excitation but did not differ consistently from non-asexuals in their sexual inhibition scores or their desire to masturbate. Content analyses supported the idea that low sexual desire is the primary feature predicting asexual identity

An action principle for the quantization of parametric theories and nonlinear quantum cosmology

By parametrizing the action integral for the standard Schrodinger equation we present a derivation of the recently proposed method for quantizing a parametrized theory. The reformulation suggests a natural extension from conventional to nonlinear quantum mechanics. This generalization enables a unitary description of the quantum evolution for a broad class of constrained Hamiltonian systems with a nonlinear kinematic structure. In particular, the new theory is applicable to the quantization of cosmological models where a chosen gravitational degree of freedom acts as geometric time. This is demonstrated explicitly using three cosmological models: the Friedmann universe with a massless scalar field and Bianchi type I and IX models. Based on these investigations, the prospect of further developing the proposed quantization scheme in the context of quantum gravity is discussed.Comment: 14 page

Optimal quantum cloning of orbital angular momentum photon qubits via Hong-Ou-Mandel coalescence

The orbital angular momentum (OAM) of light, associated with a helical structure of the wavefunction, has a great potential for quantum photonics, as it allows attaching a higher dimensional quantum space to each photon. Hitherto, however, the use of OAM has been hindered by its difficult manipulation. Here, exploiting the recently demonstrated spin-OAM information transfer tools, we report the first observation of the Hong-Ou-Mandel coalescence of two incoming photons having nonzero OAM into the same outgoing mode of a beam-splitter. The coalescence can be switched on and off by varying the input OAM state of the photons. Such effect has been then exploited to carry out the 1 \rightarrow 2 universal optimal quantum cloning of OAM-encoded qubits, using the symmetrization technique already developed for polarization. These results are finally shown to be scalable to quantum spaces of arbitrary dimension, even combining different degrees of freedom of the photons.Comment: 5 pages, 3 figure