The massive protostar W43-MM1 as seen by Herschel-HIFI water spectra: high turbulence and accretion luminosity

We present Herschel/HIFI observations of fourteen water lines in W43-MM1, a massive protostellar object in the luminous star cluster-forming region W43. We analyze the gas dynamics from the line profiles using Herschel-HIFI observations (WISH-KP) of fourteen far-IR water lines (H2O, H217O, H218O), CS(11-10), and C18O(9-8) lines, and using our modeling of the continuum spectral energy distribution. As for lower mass protostellar objects, the molecular line profiles are a mix of emission and absorption, and can be decomposed into 'medium', and 'broad' velocity components. The broad component is the outflow associated with protostars of all masses. Our modeling shows that the remainder of the water profiles can be well fitted by an infalling and passively heated envelope, with highly supersonic turbulence varying from 2.2 km/s in the inner region to 3.5 km/s in the outer envelope. Also, W43-MM1 has a high accretion rate, between 4.0 x 10^{-4} and 4.0 x 10^{-2} \msun /yr, derived from the fast (0.4-2.9 km/s) infall observed. We estimate a lower mass limit of gaseous water of 0.11 \msun and total water luminosity of 1.5 \lsun (in the 14 lines presented here). The central hot core is detected with a water abundance of 1.4 x 10^{-4} while the water abundance for the outer envelope is 8 x10^{-8}. The latter value is higher than in other sources, most likely related to the high turbulence and the micro-shocks created by its dissipation. Examining water lines of various energies, we find that the turbulent velocity increases with the distance to the center. While not in clear disagreement with the competitive accretion scenario, this behavior is predicted by the turbulent core model. Moreover, the estimated accretion rate is high enough to overcome the expected radiation pressure.Comment: Accepted in A&A on April 2, 2012. 12 pages 7 figure

First detection of ND in the solar-mass protostar IRAS16293-2422

In the past decade, much progress has been made in characterising the processes leading to the enhanced deuterium fractionation observed in the ISM and in particular in the cold, dense parts of star forming regions such as protostellar envelopes. Very high molecular D/H ratios have been found for saturated molecules and ions. However, little is known about the deuterium fractionation in radicals, even though simple radicals often represent an intermediate stage in the formation of more complex, saturated molecules. The imidogen radical NH is such an intermediate species for the ammonia synthesis in the gas phase. Herschel/HIFI represents a unique opportunity to study the deuteration and formation mechanisms of such species, which are not observable from the ground. We searched here for the deuterated radical ND in order to determine the deuterium fractionation of imidogen and constrain the deuteration mechanism of this species. We observed the solar-mass Class 0 protostar IRAS16293-2422 with the heterodyne instrument HIFI as part of the Herschel key programme CHESS (Chemical HErschel Surveys of Star forming regions). The deuterated form of the imidogen radical ND was detected and securely identified with 2 hyperfine component groups of its fundamental transition in absorption against the continuum background emitted from the nascent protostar. The 3 groups of hyperfine components of its hydrogenated counterpart NH were also detected in absorption. We derive a very high deuterium fractionation with an [ND]/[NH] ratio of between 30 and 100%. The deuterium fractionation of imidogen is of the same order of magnitude as that in other molecules, which suggests that an efficient deuterium fractionation mechanism is at play. We discuss two possible formation pathways for ND, by means of either the reaction of N+ with HD, or deuteron/proton exchange with NH.Comment: Accepted; To appear in A&A Herschel/HIFI Special Issu

Sediment source fingerprinting: benchmarking recent outputs, remaining challenges and emerging themes

Abstract: Purpose: This review of sediment source fingerprinting assesses the current state-of-the-art, remaining challenges and emerging themes. It combines inputs from international scientists either with track records in the approach or with expertise relevant to progressing the science. Methods: Web of Science and Google Scholar were used to review published papers spanning the period 2013–2019, inclusive, to confirm publication trends in quantities of papers by study area country and the types of tracers used. The most recent (2018–2019, inclusive) papers were also benchmarked using a methodological decision-tree published in 2017. Scope: Areas requiring further research and international consensus on methodological detail are reviewed, and these comprise spatial variability in tracers and corresponding sampling implications for end-members, temporal variability in tracers and sampling implications for end-members and target sediment, tracer conservation and knowledge-based pre-selection, the physico-chemical basis for source discrimination and dissemination of fingerprinting results to stakeholders. Emerging themes are also discussed: novel tracers, concentration-dependence for biomarkers, combining sediment fingerprinting and age-dating, applications to sediment-bound pollutants, incorporation of supportive spatial information to augment discrimination and modelling, aeolian sediment source fingerprinting, integration with process-based models and development of open-access software tools for data processing. Conclusions: The popularity of sediment source fingerprinting continues on an upward trend globally, but with this growth comes issues surrounding lack of standardisation and procedural diversity. Nonetheless, the last 2 years have also evidenced growing uptake of critical requirements for robust applications and this review is intended to signpost investigators, both old and new, towards these benchmarks and remaining research challenges for, and emerging options for different applications of, the fingerprinting approach

Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules

General transcription factor TFIID is a cornerstone of RNA polymerase II transcription initiation in eukaryotic cells. How human TFIID-a megadalton-sized multiprotein complex composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs)-assembles into a functional transcription factor is poorly understood. Here we describe a heterotrimeric TFIID subcomplex consisting of the TAF2, TAF8 and TAF10 proteins, which assembles in the cytoplasm. Using native mass spectrometry, we define the interactions between the TAFs and uncover a central role for TAF8 in nucleating the complex. X-ray crystallography reveals a non-canonical arrangement of the TAF8-TAF10 histone fold domains. TAF2 binds to multiple motifs within the TAF8 C-terminal region, and these interactions dictate TAF2 incorporation into a core-TFIID complex that exists in the nucleus. Our results provide evidence for a stepwise assembly pathway of nuclear holo-TFIID, regulated by nuclear import of preformed cytoplasmic submodules

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Multidimensional signals and analytic flexibility: Estimating degrees of freedom in human speech analyses

Recent empirical studies have highlighted the large degree of analytic flexibility in data analysis which can lead to substantially different conclusions based on the same data set. Thus, researchers have expressed their concerns that these researcher degrees of freedom might facilitate bias and can lead to claims that do not stand the test of time. Even greater flexibility is to be expected in fields in which the primary data lend themselves to a variety of possible operationalizations. The multidimensional, temporally extended nature of speech constitutes an ideal testing ground for assessing the variability in analytic approaches, which derives not only from aspects of statistical modeling, but also from decisions regarding the quantification of the measured behavior. In the present study, we gave the same speech production data set to 46 teams of researchers and asked them to answer the same research question, resulting insubstantial variability in reported effect sizes and their interpretation. Using Bayesian meta-analytic tools, we further find little to no evidence that the observed variability can be explained by analysts’ prior beliefs, expertise or the perceived quality of their analyses. In light of this idiosyncratic variability, we recommend that researchers more transparently share details of their analysis, strengthen the link between theoretical construct and quantitative system and calibrate their (un)certainty in their conclusions

Association and Expression Study of PRKCH Gene in a French Caucasian Population with Rheumatoid Arthritis

We study the association between three protein kinase C, eta gene polymorphisms (+8134C/T, rs912620, rs959728), and susceptibility to rheumatoid arthritis. One hundred French Caucasian rheumatoid arthritis trio families were genotyped. Relative quantification of protein kinase C, eta mRNA expression was performed from whole blood in 24 unrelated rheumatoid arthritis patients and in 16 healthy controls. Our results showed no significant association or linkage between the protein kinase C, eta polymorphisms, and rheumatoid arthritis. The protein kinase C, eta mRNA was expressed at lower level in rheumatoid arthritis unrelated patients than in healthy controls. This study shows that protein kinase C, eta gene is not a Rheumatoid Arthritis major susceptibility genetic factor in the French Caucasian population. Furthermore, the lower expression of this gene in rheumatoid arthritis patients comparing to healthy controls suggests that protein kinase C, eta could be associated with the patho-physiologic mechanism of rheumatoid arthritis