Importance of source structure on complex organics emission III. Effect of disks around massive protostars

Complex organic molecules are only detected toward a fraction of high-mass protostars. The goal of this work is to investigate whether high-mass disks can explain the lack of methanol emission from some massive protostellar systems. We consider an envelope-only and an envelope-plus-disk model and use RADMC-3D to calculate the methanol emission. High and low millimeter (mm) opacity dust are considered for both models separately and the methanol abundance is parameterized. Viscous heating is included due to the high accretion rates of these objects in the disk. In contrast with low-mass protostars, the presence of a disk does not significantly affect the temperature structure and methanol emission. The shadowing effect of the disk is not as important for high-mass objects and the disk mid-plane is hot because of viscous heating, which is effective due to the high accretion rates. Consistent with observations of infrared absorption lines toward high-mass protostars, we find a vertical temperature inversion, i.e. higher temperatures in the disk mid-plane than the disk surface, at radii < 50au for the models with $L=10^4$ L$_{\odot}$ and large mm opacity dust as long as the envelope mass is >550 M$_{\odot}$. The large observed scatter in methanol emission from massive protostars can be mostly explained toward lower luminosity objects with the envelope-plus-disk models including low and high mm opacity dust. The methanol emission variation toward sources with high luminosities cannot be explained by models with or without a disk. However, the $L/M$ of these objects suggest that they could be associated with hypercompact/ultracompact HII regions. Therefore, the low methanol emission toward the high-luminosity sources can be explained by them hosting an HII region where methanol is absent.Comment: 25 pages, 24 figures, Accepted for publication in A&

Constraining turbulence in protoplanetary discs using the gap contrast: an application to the DSHARP sample

Constraining the strength of gas turbulence in protoplanetary discs is an open problem that has relevant implications for the physics of gas accretion and planet formation. In this work, we gauge the amount of turbulence in 6 of the discs observed in the DSHARP programme by indirectly measuring the vertical distribution of their dust component. We employ the differences in the gap contrasts observed along the major and the minor axes due to projection effects, and build a radiative transfer model to reproduce these features for different values of the dust scale heights. We find that (a) the scale heights that yield a better agreement with data are generally low ($\lesssim 4$ AU at a radial distance of $100$ AU), and in almost all cases we are only able to place upper limits on their exact values; these conclusions imply (assuming an average Stokes number of $\approx10^{-2}$) low turbulence levels of $\alpha_{\rm SS}\lesssim10^{-3}-10^{-4}$; (b) for the 9 other systems we considered out of the DSHARP sample, our method yields no significant constraints on the disc vertical structure; we conclude that this is because these discs have either a low inclination or gaps that are not deep enough. Based on our analysis we provide an empirical criterion to assess whether a given disc is suitable to measure the vertical scale height.Comment: Accepted for publication in MNRAS. 13 pages + appendix, 12 figure

Predicting candidate genes for human deafness disorders: a bioinformatics approach

BACKGROUND: There are more than 50 genes for autosomal dominant and autosomal recessive nonsyndromic hereditary deafness that are yet to be cloned. The human genome sequence and expression profiles of transcripts in the inner ear have aided positional cloning approaches. The knowledge of protein interactions offers additional advantages in selecting candidate genes within a mapped region. RESULTS: We have employed a bioinformatic approach to assemble the genes encoded by genomic regions that harbor various deafness loci. The genes were then in silico analyzed for their candidacy by expression pattern and ability to interact with other proteins. Such analyses have narrowed a list of 2400 genes from suspected regions of the genome to a manageable number of about 140 for further analysis. CONCLUSION: We have established a list of strong candidate genes encoded by the regions linked to various nonsyndromic hereditary hearing loss phenotypes by using a novel bioinformatic approach. The candidates presented here provide a starting point for mutational analysis in well-characterized families along with genetic linkage to refine the loci. The advantages and shortcomings of this bioinformatic approach are discussed

Lil....

Ġabra ta’ poeżiji u proża li tinkludi: Biki ta’ Omm ta’ Dun Karm – Ras il-Pellegrin ta’ Manwel Agius – L-Aħħar Tislima ta’ Ġużè Galea – Lil Ibni Herman-Baruch ta’ Karmenu Vassallo – Flus ir-Regħba Ħajja Qasira ta’ P. P. Saydon – Frak ta’ R. M. B. – Id-Dolliegħa u l-Qargħa ta’ R. M. B. – Il-Barrakka ta’ Katrin ta’ P. Pawl Tabone – Ħniena! ta’ Fran. Camilleri – Lil.... ta’ M. Agius.N/

Musbieħ il-Lejl

Ġabra ta’ poeżiji u proża li tinkludi: Il-Gwerra ta’ Ġużè Chetcuti – B’tifkira tas-Sur Fons M. Galea ta’ P. P. Saydon – Paċi u Gwerra ta’ Dun Karm – Ħobżna ta’ Kuljum ta’ Ġużè Galea – E. Boats ta’ Dun Karm – Il-Għarqa ta’ P. Pawl Tabone – L-Għolja ta’ Ġorġ Pisani – “Air Raid” bil-Lejl ta’ J. Delia – Missirijietna u aħna ta’ Brother Amedy – Ilħna ta’ Qniepen ta’ Ġużè Chetcuti – Għanjet in-nies b'ġieħ San Duminku ta’ Mag. – Musbieħ il-Lejl ta’ Ġużè Chetcuti.N/

The distribution of accretion rates as a diagnostic of protoplanetary disc evolution

We show that the distribution of observed accretion rates is a powerful diagnostic of protoplanetary disc physics. Accretion due to turbulent ("viscous") transport of angular momentum results in a fundamentally different distribution of accretion rates than accretion driven by magnetised disc winds. We find that a homogeneous sample of $\gtrsim$300 observed accretion rates would be sufficient to distinguish between these two mechanisms of disc accretion at high confidence, even for pessimistic assumptions. Current samples of T Tauri star accretion rates are not this large, and also suffer from significant inhomogeneity, so both viscous and wind-driven models are broadly consistent with the existing observations. If accretion is viscous, the observed accretion rates require low rates of disc photoevaporation ($\lesssim$$10^{-9}$M$_{\odot}$yr$^{-1}$). Uniform, homogeneous surveys of stellar accretion rates can therefore provide a clear answer to the long-standing question of how protoplanetary discs accrete.Comment: 10 pages, 8 figures. Accepted for publication in MNRA

RNA-seq transcriptome analysis reveals long terminal repeat retrotransposon modulation in human peripheral blood mononuclear cells after in vivo lipopolysaccharide injection

Human endogenous retroviruses (HERVs) and mammalian apparent long terminal repeat (LTR) retrotransposons (MaLRs) are retroviral sequences that integrated into germ line cells millions of years ago. Transcripts of these LTR retrotransposons are present in several tissues, and their expression is modulated in pathological conditions, although their function remains often far from being understood. Here, we focused on the HERV/MaLR expression and modulation in a scenario of immune system activation. We used a public data set of human peripheral blood mononuclear cells (PBMCs) RNA-Seq from 15 healthy participants to a clinical trial before and after exposure to lipopolysaccharide (LPS), for which we established an RNA-Seq workflow for the identification of expressed and modulated cellular genes and LTR retrotransposon elements. IMPORTANCE We described the HERV and MaLR transcriptome in PBMCs, finding that about 8.4% of the LTR retrotransposon loci were expressed and identifying the betaretrovirus-like HERVs as those with the highest percentage of expressed loci. We found 4,607 HERV and MaLR loci that were modulated as a result of in vivo stimulation with LPS. The HERV-H group showed the highest number of differentially expressed most intact proviruses. We characterized the HERV and MaLR loci as differentially expressed, checking their genomic context of insertion and observing a general colocalization with genes that are involved and modulated in the immune response, as a consequence of LPS stimulation. The analyses of HERV and MaLR expression and modulation show that these LTR retrotransposons are expressed in PBMCs and regulated in inflammatory settings. The similar regulation of HERVs/MaLRs and genes after LPS stimulation suggests possible interactions of LTR retrotransposons and the immune host response

Evidence for ubiquitous carbon grain destruction in hot protostellar envelopes

Earth is deficient in carbon and nitrogen by up to ${\sim}4$ orders of magnitude compared with the Sun. Destruction of (carbon- and nitrogen-rich) refractory organics in the high-temperature planet forming regions could explain this deficiency. Assuming a refractory cometary composition for these grains, their destruction enhances nitrogen-containing oxygen-poor molecules in the hot gas ($\gtrsim 300$K) after the initial formation and sublimation of these molecules from oxygen-rich ices in the warm gas (${\sim}150$K). Using observations of $37$ high-mass protostars with ALMA, we find that oxygen-containing molecules (CH$_3$OH and HNCO) systematically show no enhancement in their hot component. In contrast, nitrogen-containing, oxygen-poor molecules (CH$_3$CN and C$_2$H$_3$CN) systematically show an enhancement of a factor ${\sim} 5$ in their hot component, pointing to additional production of these molecules in the hot gas. Assuming only thermal excitation conditions, we interpret these results as a signature of destruction of refractory organics, consistent with the cometary composition. This destruction implies a higher C/O and N/O in the hot gas than the warm gas, while, the exact values of these ratios depend on the fraction of grains that are effectively destroyed. This fraction can be found by future chemical models that constrain C/O and N/O from the abundances of minor carbon, nitrogen and oxygen carriers presented here.Comment: Accepted for publication in ApJ Letter

Suldat

Ġabra ta’ poeżiji u proża li tinkludi: Sursum Corda! ta’ R. M. B. – Tal-Qali ta’ Ġużè Ellul – Tfajla ta’ Dun Karm – Meta mort Għawdex bid-dawra ta’ Ġ. Cassar-Pullicino – Il-Maqdes tal-Mulej ta’ A. Buttigieg – Il-Barrakka ta’ Katrin ta’ P. Pawl Tabone – Ġlieġel ta’ Mary Meylak – Is-Suldat ta’ Ġużè Chetcuti.N/