Single stranded fully Modified-Phosphorothioate oligonucleotides can induce structured nuclear inclusions, alter nuclear protein localization and disturb the transcriptome In Vitro

Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2′ O- fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects

On the degree of scale invariance of inflationary perturbations

Many, if not most, inflationary models predict the power-law index of the spectrum of density perturbations is close to one, though not precisely equal to one, |n-1| \sim O(0.1), implying that the spectrum of density perturbations is nearly, but not exactly, scale invariant. Some models allow n to be significantly less than one (n \sim 0.7); a spectral index significantly greater than one is more difficult to achieve. We show that n \approx 1 is a consequence of the slow-roll conditions for inflation and ``naturalness,'' and thus is a generic prediction of inflation. We discuss what is required to deviate significantly from scale invariance, and then show, by explicit construction, the existence of smooth potentials that satisfy all the conditions for successful inflation and give $n$ as large as 2.Comment: 7 pages, 2 figures, submitted to Phys. Rev.

Cosmic Microwave Background Anisotropy with Cosine-Type Quintessence

We study the Cosmic Microwave Background (CMB) anisotropies produced by cosine-type quintessence models. In our analysis, effects of the adiabatic and isocurvature fluctuations are both taken into account. For purely adiabatic fluctuations with scale invariant spectrum, we obtain a stringent constraint on the model parameters using the CMB data from COBE, BOOMERanG and MAXIMA. Furthermore, it is shown that isocurvature fluctuations have significant effects on the CMB angular power spectrum at low multipoles in some parameter space, which may be detectable in future satellite experiments. Such a signal may be used to test the cosine-type quintessence models.Comment: 21 pages, 9 figure

Cosmic Density Perturbations from Late-Decaying Scalar Condensations

We study the cosmic density perturbations induced from fluctuation of the amplitude of late-decaying scalar condensations (called \phi) in the scenario where the scalar field \phi once dominates the universe. In such a scenario, the cosmic microwave background (CMB) radiation originates to decay products of the scalar condensation and hence its anisotropy is affected by the fluctuation of \phi. It is shown that the present cosmic density perturbations can be dominantly induced from the primordial fluctuation of \phi, not from the fluctuation of the inflaton field. This scenario may change constraints on the source of the density perturbations, like inflation. In addition, a correlated mixture of adiabatic and isocurvature perturbations may arise in such a scenario; possible signals in the CMB power spectrum are discussed. We also show that the simplest scenario of generating the cosmic density perturbations only from the primordial fluctuation of \phi (i.e., so-called ``curvaton'' scenario) is severely constrained by the current measurements of the CMB angular power spectrum if correlated mixture of the adiabatic and isocurvature perturbations are generated.Comment: 31pages, 14figure

Paraspeckle subnuclear bodies depend on dynamic heterodimerisation of DBHS RNA-binding proteins via their structured domains

RNA-binding proteins of the DBHS (Drosophila Behavior Human Splicing) family, NONO, SFPQ, and PSPC1 have numerous roles in genome stability and transcriptional and posttranscriptional regulation. Critical to DBHS activity is their recruitment to distinct subnuclear locations, for example, paraspeckle condensates, where DBHS proteins bind to the long noncoding RNA NEAT1 in the first essential step in paraspeckle formation. To carry out their diverse roles, DBHS proteins form homodimers and heterodimers, but how this dimerization influences DBHS localization and function is unknown. Here, we present an inducible GFP-NONO stable cell line and use it for live-cell 3D-structured illumination microscopy, revealing paraspeckles with dynamic, twisted elongated structures. Using siRNA knockdowns, we show these labeled paraspeckles consist of GFP-NONO/endogenous SFPQ dimers and that GFP-NONO localization to paraspeckles depends on endogenous SFPQ. Using purified proteins, we confirm that partner swapping between NONO and SFPQ occurs readily in vitro. Crystallographic analysis of the NONOSFPQ heterodimer reveals conformational differences to the other DBHS dimer structures, which may contribute to partner preference, RNA specificity, and subnuclear localization. Thus overall, our study suggests heterodimer partner availability is crucial for NONO subnuclear distribution and helps explain the complexity of both DBHS protein and paraspeckle dynamics through imaging and structural approaches.Pei Wen Lee, Andrew C. Marshall, Gavin J. Knott, Simon Kobelke, Luciano Martelotto, Ellie Cho, Paul J. McMillan, Mihwa Lee, Charles S. Bond, and Archa H. Fo

Measuring CMB Polarization with BOOMERANG

BOOMERANG is a balloon-borne telescope designed for long duration (LDB) flights around Antarctica. The second LDB Flight of BOOMERANG took place in January 2003. The primary goal of this flight was to measure the polarization of the CMB. The receiver uses polarization sensitive bolometers at 145 GHz. Polarizing grids provide polarization sensitivity at 245 and 345 GHz. We describe the BOOMERANG telescope noting changes made for 2003 LDB flight, and discuss some of the issues involved in the measurement of polarization with bolometers. Lastly, we report on the 2003 flight and provide an estimate of the expected results.Comment: 12 pages, 8 figures, To be published in the proceedings of "The Cosmic Microwave Background and its Polarization", New Astronomy Reviews, (eds. S. Hanany and K.A. Olive). Fixed typos, and reformatted citation

Gauge-ready formulation of the cosmological kinetic theory in generalized gravity theories

We present cosmological perturbations of kinetic components based on relativistic Boltzmann equations in the context of generalized gravity theories. Our general theory considers an arbitrary number of scalar fields generally coupled with the gravity, an arbitrary number of mutually interacting hydrodynamic fluids, and components described by the relativistic Boltzmann equations like massive/massless collisionless particles and the photon with the accompanying polarizations. We also include direct interactions among fluids and fields. The background FLRW model includes the general spatial curvature and the cosmological constant. We consider three different types of perturbations, and all the scalar-type perturbation equations are arranged in a gauge-ready form so that one can implement easily the convenient gauge conditions depending on the situation. In the numerical calculation of the Boltzmann equations we have implemented four different gauge conditions in a gauge-ready manner where two of them are new. By comparing solutions solved separately in different gauge conditions we can naturally check the numerical accuracy.Comment: 26 pages, 9 figures, revised thoroughly, to appear in Phys. Rev.

Bayesian joint estimation of non-Gaussianity and the power spectrum

We propose a rigorous, non-perturbative, Bayesian framework which enables one jointly to test Gaussianity and estimate the power spectrum of CMB anisotropies. It makes use of the Hilbert space of an harmonic oscillator to set up an exact likelihood function, dependent on the power spectrum and on a set of parameters $\alpha_i$, which are zero for Gaussian processes. The latter can be expressed as series of cumulants; indeed they perturbatively reduce to cumulants. However they have the advantage that their variation is essentially unconstrained. Any truncation(i.e.: finite set of $\alpha_i$) therefore still produces a proper distribution - something which cannot be said of the only other such tool on offer, the Edgeworth expansion. We apply our method to Very Small Array (VSA) simulations based on signal Gaussianity, showing that our algorithm is indeed not biased.Comment: 11pages, 4 figures, submitted to MNRA

Next-generation test of cosmic inflation

The increasing precision of cosmological datasets is opening up new opportunities to test predictions from cosmic inflation. Here we study the impact of high precision constraints on the primordial power spectrum and show how a new generation of observations can provide impressive new tests of the slow-roll inflation paradigm, as well as produce significant discriminating power among different slow-roll models. In particular, we consider next-generation measurements of the Cosmic Microwave Background (CMB) temperature anisotropies and (especially) polarization, as well as new Lyman-$\alpha$ measurements that could become practical in the near future. We emphasize relationships between the slope of the power spectrum and its first derivative that are nearly universal among existing slow-roll inflationary models, and show how these relationships can be tested on several scales with new observations. Among other things, our results give additional motivation for an all-out effort to measure CMB polarization.Comment: 10 pages, 8 figures, to appear in PRD; major changes are a reanalysis in terms of better cosmological parameters and clarifications on the contributions of polarization and Lyman-alpha dat

Detectability of Tensor Perturbations Through CBR Anisotropy (final published version)

Detection of the tensor perturbations predicted in inflationary models is important for testing inflation as well as for reconstructing the inflationary potential. We show that because of cosmic variance the tensor contribution to the square of the CBR quadrupole anisotropy must be greater than about 20\% of the scalar contribution to ensure a statistically significant detection of tensor perturbations. This sensitivity could be achieved by full-sky measurements on angular scales of $3^{\circ}$ and $0.5^\circ$.Comment: 10 pages, uu-encoded postscript file, FERMILAB-PUB-94/175-