Herschel far-infrared photometric monitoring of protostars in the Orion Nebula Cluster

We have obtained time series observations of the Orion Nebula Cluster at 70 microns and 160 microns from the Herschel/PACS Photometer. This represents the first wide-field far-infrared photometric monitoring of a young star forming region. The acquired 35'x35' maps show complex extended structures, with unprecedented details, that trace the interaction between the molecular gas and the young hot stars. We detect 43 protostars, most of which are situated along the integral-shaped filament extending from the Orion nebula, through OMC2 and to OMC3. We present high-reliability light curves for some of these objects using the first six epochs of our observing program spread over 6 weeks. We find amplitude variations in excess of 20% for a fraction of the detected protostars over periods as short as a few weeks. This is inconsistent with the dynamical time-scales of cool far-IR emitting material that orbits at hundreds of AU from the protostar, and it suggests that the mechanism(s) responsible for the observed variability originates from the inner region of the protostars, likely driven by variable mass accretion.Comment: 14 pages, 3 figures, 2 table

Infrared Variability of Evolved Protoplanetary Disks: Evidence for Scale Height Variations in the Inner Disk

We present the results of a multi-wavelength multi-epoch survey of five evolved protoplanetary disks in the IC 348 cluster that show significant infrared variability. Using 3-8micron and 24micron photometry along with 5-40micron spectroscopy from the Spitzer Space Telescope, as well as ground-based 0.8-5micron spectroscopy, optical spectroscopy and near-infrared photometry, covering timescales of days to years, we examine the variability in the disk, stellar and accretion flux. We find substantial variations (10-60%) at all infrared wavelengths on timescales of weeks to months for all of these young stellar objects. This behavior is not unique when compared to other cluster members and is consistent with changes in the structure of the inner disk, most likely scale height fluctuations on a dynamical timescale. Previous observations, along with our near-infrared photometry, indicate that the stellar fluxes are relatively constant; stellar variability does not appear to drive the large changes in the infrared fluxes. Based on our near-infrared spectroscopy of the Pa-beta and Br-gamma lines we find that the accretion rates are variable in most of the evolved disks but the overall rates are probably too small to cause the infrared variability. We discuss other possible physical causes for the variability, including the influence of a companion, magnetic fields threading the disk, and X-ray flares.Comment: Accepted to ApJ. 33 pages, emulate apj forma

Rapid Mid-Infrared Variability in Protostellar Disks

Spectral energy distribution (SED) in protostellar disks is determined by the disks'internal dissipation and reprocessing of irradiation from their host stars. Around T Tauri stars, most mid-infrared (MIR) radiation (in a few to a few ten {\mu}m wavelength range) emerge from regions around a fraction to a few AU's. This region is interesting because it contains both the habitable zone and the snow line. Recent observations reveal that SED variations, in the MIR wavelength range. These variations are puzzling because they occur on time scale (a few days) which is much shorter than the dynamical (months to years) time scale at 1AU to a few AU's. They are probably caused by shadows casted by inner onto outer disk regions. Interaction between disks and their misaligned magnetized host stars can lead to warped structure and periodic SED modulations. Rapid aperiodic SED variations may also be induced by observed X-ray flares from T Tauri stars. These flares can significantly modulate the ionization fraction of the gas and the net charge carried by the grains near the surface of the inner disk. The newly charged grains may be accelerated by the stellar or disk magnetic field and adjust their distances from the midplane. Shadows casted by these grains attenuates the flux of stellar photons irradiated onto regions at several AU's from the central stars. We use this model to account for the observed rapid aperiodic SED variabilities. We suggest regular monitoring of SED variations will not only provide valuable information on the distribution of the disk aspect ratio near the habitable zone but also provide a probe on the interaction between the inner regions of the disk with the magnetosphere of their host stars.Comment: 23 pages, 7 figure

YSOVAR: Mid-infrared Variability Among YSOs in the Star Formation Region GGD 12-15

S. J. Wolk, et al., “YSOVAR: Mid-infrared Variability Among YSOs in the Star Formation Region GGD 12-15”, The Astronomical Journal, Vol. 150(5), October 2015. © 2015. The American Astronomical Society. All rights reserved.We present an IR-monitoring survey with the $Spitzer$ Space Telescope of the star forming region GGD 12-15. Over 1000 objects were monitored including about 350 objects within the central 5 arcminutes which is found to be especially dense in cluster members. The monitoring took place over 38 days and is part of the Young Stellar Object VARiability (YSOVAR) project. The region was also the subject of a contemporaneous 67ks $Chandra$ observation. The field includes 119 previously identified pre-main sequence star candidates. X-rays are detected from 164 objects, 90 of which are identified with cluster members. Overall, we find that about half the objects in the central 5 arcminutes are young stellar objects based on a combination of their spectral energy distribution, IR variability and X-ray emission. Most of the stars with IR excess relative to a photosphere show large amplitude (>0.1 mag) mid-IR variability. There are 39 periodic sources, all but one of these is found to be a cluster member. Almost half of the periodic sources do not show IR excesses. Overall, more than 85% of the Class I, flat spectrum, and Class II sources are found to vary. The amplitude of the variability is larger in more embedded young stellar objects. Most of the Class~I/II objects exhibit redder colors in a fainter state, compatible with time-variable extinction. A few become bluer when fainter, which can be explained with significant changes in the structure of the inner disk. A search for changes in the IR due to X-ray events is carried out, but the low number of flares prevented an analysis of the direct impact of X-ray flares on the IR lightcurves. However, we find that X-ray detected Class II sources have longer timescales for change in the mid-IR than a similar set of non-X-ray detected Class IIs.Peer reviewe

The Peripheral Blood Transcriptome Identifies the Presence and Extent of Disease in Idiopathic Pulmonary Fibrosis

<div><h3>Rationale</h3><p>Peripheral blood biomarkers are needed to identify and determine the extent of idiopathic pulmonary fibrosis (IPF). Current physiologic and radiographic prognostic indicators diagnose IPF too late in the course of disease. We hypothesize that peripheral blood biomarkers will identify disease in its early stages, and facilitate monitoring for disease progression.</p> <h3>Methods</h3><p>Gene expression profiles of peripheral blood RNA from 130 IPF patients were collected on Agilent microarrays. Significance analysis of microarrays (SAM) with a false discovery rate (FDR) of 1% was utilized to identify genes that were differentially-expressed in samples categorized based on percent predicted D_LCO and FVC.</p> <h3>Main Measurements and Results</h3><p>At 1% FDR, 1428 genes were differentially-expressed in mild IPF (D_LCO >65%) compared to controls and 2790 transcripts were differentially- expressed in severe IPF (D_LCO >35%) compared to controls. When categorized by percent predicted D_LCO, SAM demonstrated 13 differentially-expressed transcripts between mild and severe IPF (< 5% FDR). These include CAMP, CEACAM6, CTSG, DEFA3 and A4, OLFM4, HLTF, PACSIN1, GABBR1, IGHM, and 3 unknown genes. Principal component analysis (PCA) was performed to determine outliers based on severity of disease, and demonstrated 1 mild case to be clinically misclassified as a severe case of IPF. No differentially-expressed transcripts were identified between mild and severe IPF when categorized by percent predicted FVC.</p> <h3>Conclusions</h3><p>These results demonstrate that the peripheral blood transcriptome has the potential to distinguish normal individuals from patients with IPF, as well as extent of disease when samples were classified by percent predicted D_LCO, but not FVC.</p> </div

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

The Saccharomyces cerevisiae Histone Chaperone Rtt106 Mediates the Cell Cycle Recruitment of SWI/SNF and RSC to the HIR-Dependent Histone Genes

In Saccharomyces cerevisiae, three out of the four histone gene pairs (HTA1-HTB1, HHT1-HHF1, and HHT2-HHF2) are regulated by the HIR co-repressor complex. The histone chaperone Rtt106 has recently been shown to be present at these histone gene loci throughout the cell cycle in a HIR- and Asf1-dependent manner and involved in their transcriptional repression. The SWI/SNF and RSC chromatin remodeling complexes are both recruited to the HIR-dependent histone genes; SWI/SNF is required for their activation in S phase, whereas RSC is implicated in their repression outside of S phase. Even though their presence at the histone genes is dependent on the HIR complex, their specific recruitment has not been well characterized. In this study we focused on characterizing the role played by the histone chaperone Rtt106 in the cell cycle-dependent recruitment of SWI/SNF and RSC complexes to the histone genes.Using GST pull-down and co-immunoprecipitation assays, we showed that Rtt106 physically interacts with both the SWI/SNF and RSC complexes in vitro and in vivo. We then investigated the function of this interaction with respect to the recruitment of these complexes to HIR-dependent histone genes. Using chromatin immunoprecipitation assays (ChIP), we found that Rtt106 is important for the recruitment of both SWI/SNF and RSC complexes to the HIR-dependent histone genes. Furthermore, using synchronized cell cultures, we showed by ChIP assays that the Rtt106-dependent SWI/SNF recruitment to these histone gene loci is cell cycle regulated and restricted to late G1 phase just before the peak of histone gene expression in S phase.Overall, these data strongly suggest that the interaction between the histone chaperone Rtt106 and both the SWI/SNF and RSC chromatin remodeling complexes is important for the cell cycle regulated recruitment of these two complexes to the HIR-dependent histone genes

The Use of Flagella and Motility for Plant Colonization and Fitness by Different Strains of the Foodborne Pathogen Listeria monocytogenes

The role of flagella and motility in the attachment of the foodborne pathogen Listeria monocytogenes to various surfaces is mixed with some systems requiring flagella for an interaction and others needing only motility for cells to get to the surface. In nature this bacterium is a saprophyte and contaminated produce is an avenue for infection. Previous studies have documented the ability of this organism to attach to and colonize plant tissue. Motility mutants were generated in three wild type strains of L. monocytogenes by deleting either flaA, the gene encoding flagellin, or motAB, genes encoding part of the flagellar motor, and tested for both the ability to colonize sprouts and for the fitness of that colonization. The motAB mutants were not affected in the colonization of alfalfa, radish, and broccoli sprouts; however, some of the flaA mutants showed reduced colonization ability. The best colonizing wild type strain was reduced in colonization on all three sprout types as a result of a flaA deletion. A mutant in another background was only affected on alfalfa. The third, a poor alfalfa colonizer was not affected in colonization ability by any of the deletions. Fitness of colonization was measured in experiments of competition between mixtures of mutant and parent strains on sprouts. Here the flaA and motAB mutants of the three strain backgrounds were impaired in fitness of colonization of alfalfa and radish sprouts, and one strain background showed reduced fitness of both mutant types on broccoli sprouts. Together these data indicate a role for flagella for some strains to physically colonize some plants, while the fitness of that colonization is positively affected by motility in almost all cases

The crucial role of particle surface reactivity in respirable quartz-induced reactive oxygen/nitrogen species formation and APE/Ref-1 induction in rat lung

Persistent inflammation and associated excessive oxidative stress have been crucially implicated in quartz-induced pulmonary diseases, including fibrosis and cancer. We have investigated the significance of the particle surface reactivity of respirable quartz dust in relation to the in vivo generation of reactive oxygen and nitrogen species (ROS/RNS) and the associated induction of oxidative stress responses in the lung. Therefore, rats were intratracheally instilled with 2 mg quartz (DQ12) or quartz whose surface was modified by either polyvinylpyridine-N-oxide (PVNO) or aluminium lactate (AL). Seven days after instillation, the bronchoalveolar lavage fluid (BALF) was analysed for markers of inflammation (total/differential cell counts), levels of pulmonary oxidants (H(2)O(2), nitrite), antioxidant status (trolox equivalent antioxidant capacity), as well as for markers of lung tissue damage, e.g. total protein, lactate dehydrogenase and alkaline phosphatase. Lung homogenates as well as sections were investigated regarding the induction of the oxidative DNA-lesion/oxidative stress marker 8-hydroxy-2'-deoxyguanosine (8-OHdG) using HPLC/ECD analysis and immunohistochemistry, respectively. Homogenates and sections were also investigated for the expression of the bifunctional apurinic/apyrimidinic endonuclease/redox factor-1 (APE/Ref-1) by Western blotting and immunohistochemistry. Significantly increased levels of H(2)O(2 )and nitrite were observed in rats treated with non-coated quartz, when compared to rats that were treated with either saline or the surface-modified quartz preparations. In the BALF, there was a strong correlation between the number of macrophages and ROS, as well as total cells and RNS. Although enhanced oxidant generation in non-coated DQ12-treated rats was paralleled with an increased total antioxidant capacity in the BALF, these animals also showed significantly enhanced lung tissue damage. Remarkably however, elevated ROS levels were not associated with an increase in 8-OHdG, whereas the lung tissue expression of APE/Ref-1 protein was clearly up-regulated. The present data provide further in vivo evidence for the crucial role of particle surface properties in quartz dust-induced ROS/RNS generation by recruited inflammatory phagocytes. Our results also demonstrate that quartz dust can fail to show steady-state enhanced oxidative DNA damage in the respiratory tract, in conditions were it elicits a marked and persistent inflammation with associated generation of ROS/RNS, and indicate that this may relate to compensatory induction of APE/Ref-1 mediated base excision repair