90 research outputs found
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 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 \%, increasing to a few percent at the
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
Evolution of envelope sequences of human immunodeficiency virus type 1 in cellular reservoirs in the setting of potent antiviral therapy
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
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