Simultaneous Determination of the Cosmic Ray Ionization Rate and Fractional Ionization in DR21(OH)

We present a new method for the simultaneous calculation of the cosmic ray ionization rate, zeta(H2), and the ionization fraction, chi(e), in dense molecular clouds. A simple network of chemical reactions dominant in the creation and destruction of HCNH+ and HCO+ is used in conjunction with observed pairs of rotational transitions of several molecular species in order to determine the electron abundance and the H3+ abundance. The cosmic ray ionization rate is then calculated by taking advantage of the fact that, in dark clouds, it governs the rate of creation of H3+. We apply this technique to the case of the star-forming region DR21(OH), where we successfully detected the (J=3-2) and (J=4-3) rotational transitions of HCNH+. We also determine the C and O isotopic ratios in this source to be 12C/13C=63+-4 and 16O/18O=318+-64, which are in good agreement with previous measurements in other clouds. The significance of our method lies in the ability to determine N(H3+) and chi(e) directly from observations, and estimate zeta(H2) accordingly. Our results, zeta(H2)=3.1x10^(-18) 1/s and chi(e)=3.2x10^(-8), are consistent with recent determinations in other objects.Comment: 22 pages, including 3 figure

Submillimeter Polarimetry with PolKa, a reflection-type modulator for the APEX telescope

Imaging polarimetry is an important tool for the study of cosmic magnetic fields. In our Galaxy, polarization levels of a few up to $\sim$10\% are measured in the submillimeter dust emission from molecular clouds and in the synchrotron emission from supernova remnants. Only few techniques exist to image the distribution of polarization angles, as a means of tracing the plane-of-sky projection of the magnetic field orientation. At submillimeter wavelengths, polarization is either measured as the differential total power of polarization-sensitive bolometer elements, or by modulating the polarization of the signal. Bolometer arrays such as LABOCA at the APEX telescope are used to observe the continuum emission from fields as large as \sim0\fdg2 in diameter. %Here we present the results from the commissioning of PolKa, a polarimeter for Here we present PolKa, a polarimeter for LABOCA with a reflection-type waveplate of at least 90\% efficiency. The modulation efficiency depends mainly on the sampling and on the angular velocity of the waveplate. For the data analysis the concept of generalized synchronous demodulation is introduced. The instrumental polarization towards a point source is at the level of $\sim0.1$\%, increasing to a few percent at the $-10$db contour of the main beam. A method to correct for its effect in observations of extended sources is presented. Our map of the polarized synchrotron emission from the Crab nebula is in agreement with structures observed at radio and optical wavelengths. The linear polarization measured in OMC1 agrees with results from previous studies, while the high sensitivity of LABOCA enables us to also map the polarized emission of the Orion Bar, a prototypical photon-dominated region

Characterisation of the Mouse Vasoactive Intestinal Peptide Receptor Type 2 Gene, Vipr2, and Identification of a Polymorphic LINE-1-like Sequence That Confers Altered Promoter Activity

The VPAC(2) receptor is a seven transmembrane spanning G protein-coupled receptor for two neuropeptides, vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP). It has a distinct tissue-specific, developmental and inducible expression that underlies an important neuroendocrine role. Here, we report the characterisation of the gene that encodes the mouse VPAC(2) receptor (Vipr2), localisation of the transcriptional start site and functional analysis of the promoter region. The Vipr2 gene contains 12 introns within its protein-coding region and spans 68.6 kb. Comparison of the 5′ untranslated region sequences for cloned 5′-RACE products amplified from different tissues showed they all were contained within the same exon, with the longest extending 111 bp upstream of the ATG start site. Functional analysis of the 3.2-kb 5′-flanking region using sequentially deleted sequences cloned into a luciferase gene reporter vector revealed that this region is active as a promoter in mouse AtT20 D16:16 and rat GH4C1 cell lines. The core promoter is located within a 180-bp GC-rich region proximal to the ATG start codon and contains potential binding sites for Sp1 and AP2, but no TATA-box. Further upstream, in two out of three mice strains examined, we have discovered a 496-bp polymorphic DNA sequence that bears a significant identity to mouse LINE-1 DNA. Comparison of the promoter activity between luciferase reporter gene constructs derived from the BALB/c (which contains this sequence) and C57BL/6J (which lacks this sequence) Vipr2 promoter regions has shown three-fold difference in luciferase gene activity when expressed in mouse AtT20 D16:16 and αT3-1 cells, but not when expressed in the rat GH4C1 cells or in COS 7 cells. Our results suggest that the mouse Vipr2 gene may be differentially active in different mouse strains, depending on the presence of this LINE-1-like sequence in the promoter region

Polarisation Observations of VY Canis Majoris Water Vapour 5{32}-4{41} 620.701 GHz Maser Emission with HIFI

CONTEXT: Water vapour maser emission from evolved oxygen-rich stars remains poorly understood. Additional observations, including polarisation studies and simultaneous observation of different maser transitions may ultimately lead to greater insight. AIMS: We have aimed to elucidate the nature and structure of the VY CMa water vapour masers in part by observationally testing a theoretical prediction of the relative strengths of the 620.701 GHz and the 22.235 GHz maser components of ortho water vapour. METHODS: In its high-resolution mode (HRS) the Herschel Heterodyne Instrument for the Infrared (HIFI) offers a frequency resolution of 0.125 MHz, corresponding to a line-of-sight velocity of 0.06 km/s, which we employed to obtain the strength and linear polarisation of maser spikes in the spectrum of VY CMa at 620.701 GHz. Simultaneous ground based observations of the 22.235 GHz maser with the Max-Planck-Institut f\"ur Radioastronomie 100-meter telescope at Effelsberg, provided a ratio of 620.701 GHz to 22.235 GHz emission. RESULTS:We report the first astronomical detection to date of water vapour maser emission at 620.701 GHz. In VY CMa both the 620.701 and the 22.235 GHz polarisation are weak. At 620.701 GHz the maser peaks are superposed on what appears to be a broad emission component, jointly ejected asymmetrically from the star. We observed the 620.701 GHz emission at two epochs 21 days apart, both to measure the potential direction of linearly polarised maser components and to obtain a measure of the longevity of these components. Although we do not detect significant polarisation levels in the core of the line, they rise up to approximately 6% in its wings

Cosmic-ray propagation in molecular clouds

Cosmic-rays constitute the main ionising and heating agent in dense, starless, molecular cloud cores. We reexamine the physical quantities necessary to determine the cosmic-ray ionisation rate (especially the cosmic ray spectrum at E < 1 GeV and the ionisation cross sections), and calculate the ionisation rate as a function of the column density of molecular hydrogen. Available data support the existence of a low-energy component (below about 100 MeV) of cosmic-ray electrons or protons responsible for the ionisation of diffuse and dense clouds. We also compute the attenuation of the cosmic-ray flux rate in a cloud core taking into account magnetic focusing and magnetic mirroring, following the propagation of cosmic rays along flux tubes enclosing different amount of mass and mass-to-flux ratios. We find that mirroring always dominates over focusing, implying a reduction of the cosmic-ray ionisation rate by a factor of 3-4 depending on the position inside the core and the magnetisation of the core.Comment: To appear in "Cosmic Rays in Star-Forming Environments", Proceedings of the 2nd Session of the Sant Cugat Forum on Astrophysics. D. F. Torres and O. Reimer (Editors), 2013, Springer, 25 pages, 11 figure

Cosmic-ray ionization of molecular clouds

Low-energy cosmic rays are a fundamental source of ionization for molecular clouds, influencing their chemical, thermal and dynamical evolution. The purpose of this work is to explore the possibility that a low-energy component of cosmic-rays, not directly measurable from the Earth, can account for the discrepancy between the ionization rate measured in diffuse and dense interstellar clouds. We collect the most recent experimental and theoretical data on the cross sections for the production of H2+ and He+ by electron and proton impact, and we discuss the available constraints on the cosmic-ray fluxes in the local interstellar medium. Starting from different extrapolations at low energies of the demodulated cosmic-ray proton and electron spectra, we compute the propagated spectra in molecular clouds in the continuous slowing-down approximation taking into account all the relevant energy loss processes. The theoretical value of the cosmic-ray ionization rate as a function of the column density of traversed matter is in agreement with the observational data only if either the flux of cosmic-ray electrons or of protons increases at low energies. The most successful models are characterized by a significant (or even dominant) contribution of the electron component to the ionization rate, in agreement with previous suggestions. However, the large spread of cosmic-ray ionization rates inferred from chemical models of molecular cloud cores remains to be explained. Available data combined with simple propagation models support the existence of a low-energy component (below about 100 MeV) of cosmic-ray electrons or protons responsible for the ionization of molecular cloud cores and dense protostellar envelopes.Comment: 14 pages, 15 figure

Molecular Tracers of Turbulent Shocks in Giant Molecular Clouds

Giant molecular clouds contain supersonic turbulence and simulations of magnetohydrodynamic turbulence show that these supersonic motions decay in roughly a crossing time, which is less than the estimated lifetimes of molecular clouds. Such a situation requires a significant release of energy. We run models of C-type shocks propagating into gas with densities around 10^3 cm^(-3) at velocities of a few km / s, appropriate for the ambient conditions inside of a molecular cloud, to determine which species and transitions dominate the cooling and radiative energy release associated with shock cooling of turbulent molecular clouds. We find that these shocks dissipate their energy primarily through CO rotational transitions and by compressing pre-existing magnetic fields. We present model spectra for these shocks and by combining these models with estimates for the rate of turbulent energy dissipation, we show that shock emission should dominate over emission from unshocked gas for mid to high rotational transitions (J >5) of CO. We also find that the turbulent energy dissipation rate is roughly equivalent to the cosmic-ray heating rate and that the ambipolar diffusion heating rate may be significant, especially in shocked gas.Comment: 14 pages, 5 figures, accepted for publication in ApJ; minor grammatical errors correcte

Effects of prostratin on Cyclin T1/P-TEFb function and the gene expression profile in primary resting CD4(+ )T cells

BACKGROUND: The latent reservoir of human immunodeficiency virus type 1 (HIV-1) in resting CD4(+ )T cells is a major obstacle to the clearance of infection by highly active antiretroviral therapy (HAART). Recent studies have focused on searches for adjuvant therapies to activate this reservoir under conditions of HAART. Prostratin, a non tumor-promoting phorbol ester, is a candidate for such a strategy. Prostratin has been shown to reactivate latent HIV-1 and Tat-mediated transactivation may play an important role in this process. We examined resting CD4(+ )T cells from healthy donors to determine if prostratin induces Cyclin T1/P-TEFb, a cellular kinase composed of Cyclin T1 and Cyclin-dependent kinase-9 (CDK9) that mediates Tat function. We also examined effects of prostratin on Cyclin T2a, an alternative regulatory subunit for CDK9, and 7SK snRNA and the HEXIM1 protein, two factors that associate with P-TEFb and repress its kinase activity. RESULTS: Prostratin up-regulated Cyclin T1 protein expression, modestly induced CDK9 protein expression, and did not affect Cyclin T2a protein expression. Although the kinase activity of CDK9 in vitro was up-regulated by prostratin, we observed a large increase in the association of 7SK snRNA and the HEXIM1 protein with CDK9. Using HIV-1 reporter viruses with and without a functional Tat protein, we found that prostratin stimulation of HIV-1 gene expression appears to require a functional Tat protein. Microarray analyses were performed and several genes related to HIV biology, including APOBEC3B, DEFA1, and S100 calcium-binding protein genes, were found to be regulated by prostratin. CONCLUSION: Prostratin induces Cyclin T1 expression and P-TEFb function and this is likely to be involved in prostratin reactivation of latent HIV-1 proviruses. The large increase in association of 7SK and HEXIM1 with P-TEFb following prostratin treatment may reflect a requirement in CD4(+ )T cells for a precise balance between active and catalytically inactive P-TEFb. Additionally, genes regulated by prostratin were identified that have the potential to regulate HIV-1 replication both positively and negatively

De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes

Background Euphorbia fischeriana is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbol ester from the tigliane diterpene series. Prostratin is a protein kinase C activator and is effective in the treatment of Human Immunodeficiency Virus (HIV) by acting as a latent HIV activator. Latent HIV is currently the biggest limitation for viral eradication. The aim of this study was to sequence, assemble and annotate the E. fischeriana transcriptome to better understand the potential biochemical pathways leading to the synthesis of prostratin and other related diterpene compounds. Results In this study we conducted a high throughput RNA-seq approach to sequence the root transcriptome of E. fischeriana. We assembled 18,180 transcripts, of these the majority encoded protein-coding genes and only 17 transcripts corresponded to known RNA genes. Interestingly, we identified 5,956 protein-coding transcripts with high similarity (>=75%) to Ricinus communis, a close relative to E. fischeriana. We also evaluated the conservation of E. fischeriana genes against EST datasets from the Euphorbeacea family, which included R. communis, Hevea brasiliensis and Euphorbia esula. We identified a core set of 1,145 gene clusters conserved in all four species and 1,487 E. fischeriana paralogous genes. Furthermore, we screened E. fischeriana transcripts against an in-house reference database for genes implicated in the biosynthesis of upstream precursors to prostratin. This identified 24 and 9 candidate transcripts involved in the terpenoid and diterpenoid biosyntehsis pathways, respectively. The majority of the candidate genes in these pathways presented relatively low expression levels except for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (HDS) and isopentenyl diphosphate/dimethylallyl diphosphate synthase (IDS), which are required for multiple downstream pathways including synthesis of casbene, a proposed precursor to prostratin. Conclusion The resources generated in this study provide new insights into the upstream pathways to the synthesis of prostratin and will likely facilitate functional studies aiming to produce larger quantities of this compound for HIV research and/or treatment of patients