Emission from Water Vapor and Absorption from Other Gases at 5-7.5 Microns in Spitzer-IRS Spectra of Protoplanetary Disks

We present spectra of 13 T Tauri stars in the Taurus-Auriga star-forming region showing emission in Spitzer Space Telescope Infrared Spectrograph (IRS) 5-7.5 micron spectra from water vapor and absorption from other gases in these stars' protoplanetary disks. Seven stars' spectra show an emission feature at 6.6 microns due to the nu_2 = 1-0 bending mode of water vapor, with the shape of the spectrum suggesting water vapor temperatures > 500 K, though some of these spectra also show indications of an absorption band, likely from another molecule. This water vapor emission contrasts with the absorption from warm water vapor seen in the spectrum of the FU Orionis star V1057 Cyg. The other six of the thirteen stars have spectra showing a strong absorption band, peaking in strength at 5.6-5.7 microns, which for some is consistent with gaseous formaldehyde (H2CO) and for others is consistent with gaseous formic acid (HCOOH). There are indications that some of these six stars may also have weak water vapor emission. Modeling of these stars' spectra suggests these gases are present in the inner few AU of their host disks, consistent with recent studies of infrared spectra showing gas in protoplanetary disks.Comment: 33 pages, 9 figures, to appear in the 20 August, 2014, V791 - 2 issue of the Astrophysical Journa

Millimeter imaging of HD 163296: probing the disk structure and kinematics

We present new multi-wavelength millimeter interferometric observations of the Herbig Ae star HD 163296 obtained with the IRAM/PBI, SMA and VLA arrays both in continuum and in the 12CO, 13CO and C18O emission lines. Gas and dust properties have been obtained comparing the observations with self-consistent disk models for the dust and CO emission. The circumstellar disk is resolved both in the continuum and in CO. We find strong evidence that the circumstellar material is in Keplerian rotation around a central star of 2.6 Msun. The disk inclination with respect to the line of sight is 46+-4 deg with a position angle of 128+-4 deg. The slope of the dust opacity measured between 0.87 and 7 mm (beta=1) confirms the presence of mm/cm-size grains in the disk midplane. The dust continuum emission is asymmetric and confined inside a radius of 200 AU while the CO emission extends up to 540 AU. The comparison between dust and CO temperature indicates that CO is present only in the disk interior. Finally, we obtain an increasing depletion of CO isotopomers from 12CO to 13CO and C18O. We argue that these results support the idea that the disk of HD 163296 is strongly evolved. In particular, we suggest that there is a strong depletion of dust relative to gas outside 200 AU; this may be due to the inward migration of large bodies that form in the outer disk or to clearing of a large gap in the dust distribution by a low mass companion.Comment: Accepted for publication on A&A, 16 page

Analysis of Lipid-linked Oligosaccharides Synthesized in vivo in Schizosaccharomyces pombe

Dolichol diphosphate-linked oligosaccharides (LLO) are the sugar donors in N-glycosylation, a fundamental protein post-translational modification of the eukaryotic secretory pathway. Defects in LLO biosynthesis produce human Congenital Disorders of Glycosylation Type I. The synthesis of LLOs and the transfer reactions to their protein acceptors is highly conserved among animal, plant, and fungi kingdoms, making the fission yeast Schizosaccharomyces pombe a suitable model to study these processes. Here, we present a protocol to determine the LLO patterns produced in vivo by S. pombe cells that may be easily adapted to other cell types. First, exponentially growing cultures are labeled with a pulse of [14C]-glucose. LLOs are then purified by successive extractions with organic solvents, and glycans are separated from the lipid moieties in mild acid hydrolysis and a new solvent extraction. The purified glycans are then run on paper chromatography. We use a deconvolution process to adjust the profile obtained to the minimal number of Gaussian functions needed to fit the data and determine the proportion of each species with respect to total glycan species present in the cell. The method we provide here might be used without any expensive or specialized equipment. The deconvolution process described here might also be useful to analyze species in non-completely resolved chromatograms.Fil: Valko, Ayelén. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biociencias, Biotecnología y Biología Traslacional; ArgentinaFil: Gallo, Giovanna Lucrecia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biociencias, Biotecnología y Biología Traslacional; Argentina. Ministerio de Producción y Trabajo. Secretaría de Gobierno de Agroindustria. Servicio Nacional de Sanidad y Calidad Agroalimentaria. Centro de Virología Humana y Animal. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Centro de Virología Humana y Animal; ArgentinaFil: Weisz, Ariel D.. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biociencias, Biotecnología y Biología Traslacional; ArgentinaFil: Parodi, Armando José A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: D'alessio, Cecilia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biociencias, Biotecnología y Biología Traslacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Engineered Sleeping Beauty Transposon as Efficient System to Optimize Chimp Adenoviral Production

Sleeping Beauty (SB) is the first DNA transposon employed for efficient transposition in vertebrate cells, opening new applications for genetic engineering and gene therapies. A transposon-based gene delivery system holds the favourable features of non-viral vectors and an attractive safety profile. Here, we employed SB to engineer HEK293 cells for optimizing the production of a chimpanzee Adenovector (chAd) belonging to the Human Mastadenovirus C species. To date, chAd vectors are employed in several clinical settings for infectious diseases, last but not least COVID-19. A robust, efficient and quick viral vector production could advance the clinical application of chAd vectors. To this aim, we firstly swapped the hAd5 E1 with chAd-C E1 gene by using the CRISPR/Cas9 system. We demonstrated that in the absence of human Ad5 E1, chimp Ad-C E1 gene did not support HEK293 survival. To improve chAd-C vector production, we engineered HEK293 cells to stably express the chAd-C precursor terminal protein (ch.pTP), which plays a crucial role in chimpanzee Adenoviral DNA replication. The results indicate that exogenous ch.pTP expression significantly ameliorate the packaging and amplification of recombinant chAd-C vectors thus, the engineered HEK293ch.pTP cells could represent a superior packaging cell line for the production of these vectors

The Spitzer Infrared Spectrograph Survey of T Tauri Stars in Taurus

We present 161 Spitzer Infrared Spectrograph (IRS) spectra of T Tauri stars and young brown dwarfs in the Taurus star-forming region. All of the targets were selected based on their infrared excess and are therefore surrounded by protoplanetary disks; they form the complete sample of all available IRS spectra of T Tauri stars with infrared excesses in Taurus. We also present the IRS spectra of seven Class 0/I objects in Taurus to complete the sample of available IRS spectra of protostars in Taurus. We use spectral indices that are not significantly affected by extinction to distinguish between envelope-and disk-dominated objects. Together with data from the literature, we construct spectral energy distributions for all objects in our sample. With spectral indices derived from the IRS spectra we infer disk properties such as dust settling and the presence of inner disk holes and gaps. We find a transitional disk frequency, which is based on objects with unusually large 13-31 mu m spectral indices indicative of a wall surrounding an inner disk hole, of about 3%, and a frequency of about 20% for objects with unusually large 10 mu m features, which could indicate disk gaps. The shape and strength of the 10 mu m silicate emission feature suggests weaker 10 mu m emission and more processed dust for very low mass objects and brown dwarfs (spectral types M6-M9). These objects also display weaker infrared excess emission from their disks, but do not appear to have more settled disks than their higher-mass counterparts. We find no difference for the spectral indices and properties of the dust between single and multiple systems.NASANASA through JPL/CaltechNASA through the Spitzer Space TelescopeNational Science Foundation AST-0544588, 0901947Pennsylvania State UniversityEberly College of SciencePennsylvania Space Grant ConsortiumNSFAstronom

Rotational Line Emission from Water in Protoplanetary Disks

Circumstellar disks provide the material reservoir for the growth of young stars and for planet formation. We combine a high-level radiative transfer program with a thermal-chemical model of a typical T Tauri star disk to investigate the diagnostic potential of the far-infrared lines of water for probing disk structure. We discuss the observability of pure rotational H2O lines with the Herschel Space Observatory, specifically the residual gas where water is mainly frozen out. We find that measuring both the line profile of the ground 110-101 ortho-H2O transition and the ratio of this line to the 312-303 and 221-212 line can provide information on the gas phase water between 5-100 AU, but not on the snow line which is expected to occur at smaller radii.Comment: 5 pages, 4 figures. Accepted by ApJ

Impact of grain evolution on the chemical structure of protoplanetary disks

We study the impact of dust evolution in a protoplanetary disk around a T Tauri star on the disk chemical composition. For the first time we utilize a comprehensive model of dust evolution which includes growth, fragmentation and sedimentation. Specific attention is paid to the influence of grain evolution on the penetration of the UV field in the disk. A chemical model that includes a comprehensive set of gas phase and grain surface chemical reactions is used to simulate the chemical structure of the disk. The main effect of the grain evolution on the disk chemical composition comes from sedimentation, and, to a lesser degree, from the reduction of the total grain surface area. The net effect of grain growth is suppressed by the fragmentation process which maintains a population of small grains, dominating the total grain surface area. We consider three models of dust properties. In model GS both growth and sedimentation are taken into account. In models A5 and A4 all grains are assumed to have the same size (10(-5) cm and 10(-4) cm, respectively) with constant gas-to-dust mass ratio of 100. Like in previous studies, the "three-layer" pattern (midplane, molecular layer, hot atmosphere) in the disk chemical structure is preserved in all models, but shifted closer to the midplane in models with increased grain size (GS and A4). Unlike other similar studies, we find that in models GS and A4 column densities of most gas-phase species are enhanced by 1-3 orders of magnitude relative to those in a model with pristine dust (A5), while column densities of their surface counterparts are decreased. We show that column densities of certain species, like C2H, HC(2n+1)N (n=0-3), H2O and some other molecules, as well as the C2H2/HCN abundance ratio which are accessible with Herschel and ALMA can be used as observational tracers of early stages of the grain evolution process in protoplanetary disks.Comment: 50 pages, 4 tables, 11 figures, accepted to the Ap

The Structure of the DoAr 25 Circumstellar Disk

We present high spatial resolution (< 0.3" = 40$AU) Submillimeter Array observations of the 865 micron continuum emission from the circumstellar disk around the young star DoAr 25. Despite its bright millimeter emission, this source exhibits only a comparatively small infrared excess and low accretion rate, suggesting that the material and structural properties of the inner disk may be in an advanced state of evolution. A simple model of the physical conditions in the disk is derived from the submillimeter visibilities and the complete spectral energy distribution using a Monte Carlo radiative transfer code. For the standard assumption of a homogeneous grain size distribution at all disk radii, the results indicate a shallow surface density profile,$\Sigma \propto r^{-p}$ with p = 0.34, significantly less steep than a steady-state accretion disk (p = 1) or the often adopted minimum mass solar nebula (p = 1.5). Even though the total mass of material is large (M_d = 0.10 M_sun), the densities inferred in the inner disk for such a model may be too low to facilitate any mode of planet formation. However, alternative models with steeper density gradients (p = 1) can explain the observations equally well if substantial grain growth in the planet formation region (r < 40 AU) has occurred. We discuss these data in the context of such models with dust properties that vary with radius and highlight their implications for understanding disk evolution and the early stages of planet formation.Comment: ApJL in pres