What Sets the Star Formation Rate of Molecular Clouds? The Density Distribution as a Fingerprint of Compression and Expansion Rates

We use a suite of 3D simulations of star-forming molecular clouds, with and without stellar feedback, magnetic fields, and driven turbulence, to study the compression and expansion rates of the gas as functions of density. We show that, around the mean density, supersonic turbulence promotes rough equilibrium between the amounts of compressing and expanding gas, consistent with continuous gas cycling between high- and low-density states. We find that the inclusion of protostellar jets produces rapidly expanding and compressing low-density gas. We find that the gas mass flux peaks at the transition between the lognormal and power-law forms of the density probability distribution function (PDF). This is consistent with the transition density tracking the post-shock density, which promotes an enhancement of mass at this density (i.e., shock compression and filament formation). At high densities, the gas dynamics are dominated by self-gravity: the compression rate in all of our runs matches the rate of the run with only gravity, suggesting that processes other than self-gravity have little effect at these densities. The net gas mass flux becomes constant at a density below the sink formation threshold, where it equals the star formation rate. The density at which the net gas mass flux equals the star formation rate is one order of magnitude lower than our sink threshold density, corresponds to the formation of the second power-law tail in the density PDF, and sets the overall star formation rates of these simulations

Advanced Diagnostics for the Study of Linearly Polarized Emission. II: Application to Diffuse Interstellar Radio Synchrotron Emission

Diagnostics of polarized emission provide us with valuable information on the Galactic magnetic field and the state of turbulence in the interstellar medium, which cannot be obtained from synchrotron intensity alone. In Paper I (Herron et al. 2017b), we derived polarization diagnostics that are rotationally and translationally invariant in the $Q$-$U$ plane, similar to the polarization gradient. In this paper, we apply these diagnostics to simulations of ideal magnetohydrodynamic turbulence that have a range of sonic and Alfv\'enic Mach numbers. We generate synthetic images of Stokes $Q$ and $U$ for these simulations, for the cases where the turbulence is illuminated from behind by uniform polarized emission, and where the polarized emission originates from within the turbulent volume. From these simulated images we calculate the polarization diagnostics derived in Paper I, for different lines of sight relative to the mean magnetic field, and for a range of frequencies. For all of our simulations, we find that the polarization gradient is very similar to the generalized polarization gradient, and that both trace spatial variations in the magnetoionic medium for the case where emission originates within the turbulent volume, provided that the medium is not supersonic. We propose a method for distinguishing the cases of emission coming from behind or within a turbulent, Faraday rotating medium, and a method to partly map the rotation measure of the observed region. We also speculate on statistics of these diagnostics that may allow us to constrain the physical properties of an observed turbulent region.Comment: 34 pages, 25 figures, accepted for publication in Ap

Sequence verification of synthetic DNA by assembly of sequencing reads

This is the publisher’s final pdf. The published article is copyrighted by Oxford University Press and can be found at: http://www.oxfordjournals.org/Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org

Levothyrox® new and old formulations: are they switchable for millions of patients?

International audienceIn France, more than 2.5 million patients are currently treated with levothyroxine, mainly as the marketed product Levothyrox ®. In March 2017, at the request of French authorities, a new formulation of Levothyrox ® was licensed, with the objective of avoiding stability deficiencies of the old formulation. Before launching this new formulation, an average bioequivalence trial, based on European Union recommended guidelines, was performed. The implicit rationale was the assumption that the two products, being bioequivalent, would also be switchable, allowing substitution of the new for the old formulation, thus avoiding the need for individual calibration of the dosage regimen of thyroxine, using the thyroid-stimulating hormone level as the endpoint, as required for a new patient on initiating treatment. Despite the fact that both formulations were shown to be bioequivalent, adverse drug reactions were reported in several thousands of patients after taking the new formulation. In this opinion paper, we report that more than 50% of healthy volunteers enrolled in a successful regulatory average bioequivalence trial were actually outside the a priori bioequivalence range. Therefore, we question the ability of an average bioequivalence trial to guarantee the switchability within patients of the new and old levothyroxine formulations. We further propose an analysis of this problem using the conceptual framework of individual bioequivalence. This involves investigating the bioavailability of the two formulations within a subject, by comparing not only the population means (as established by average bioequivalence) but also by assessing two variance terms, namely the within-subject variance and the variance estimating subject-by-formulation interaction. A higher within individual variability for the new formulation would lead to reconsideration of the appropriateness of the new formulation. Alternatively, a possible subject-by-formulation interaction would allow a judgement on the ability, or not, of doctors to manage patients effectively during transition from the old to the new formulation

Unveiling the Role of the Magnetic Field at the Smallest Scales of Star Formation

We report Atacama Large Millimeter/submillimeter Array (ALMA) observations of polarized dust emission from the protostellar source Ser-emb 8 at a linear resolution of 140 au. Assuming models of dust-grain alignment hold, the observed polarization pattern gives a projected view of the magnetic field structure in this source. Contrary to expectations based on models of strongly magnetized star formation, the magnetic field in Ser-emb 8 does not exhibit an hourglass morphology. Combining the new ALMA data with previous observational studies, we can connect magnetic field structure from protostellar core (̃80,000 au) to disk (̃100 au) scales. We compare our observations with four magnetohydrodynamic gravo-turbulence simulations made with the AREPO code that have initial conditions ranging from super-Alfvénic (weakly magnetized) to sub-Alfvénic (strongly magnetized). These simulations achieve the spatial dynamic range necessary to resolve the collapse of protostars from the parsec scale of star-forming clouds down to the ̃100 au scale probed by ALMA. Only in the very strongly magnetized simulation do we see both the preservation of the field direction from cloud to disk scales and an hourglass-shaped field at <1000 au scales. We conduct an analysis of the relative orientation of the magnetic field and the density structure in both the Ser-emb 8 ALMA observations and the synthetic observations of the four AREPO simulations. We conclude that the Ser-emb 8 data are most similar to the weakly magnetized simulations, which exhibit random alignment, in contrast to the strongly magnetized simulation, where the magnetic field plays a role in shaping the density structure in the source. In the weak-field case, it is turbulence—not the magnetic field—that shapes the material that forms the protostar, highlighting the dominant role that turbulence can play across many orders of magnitude in spatial scale.Astronom

The completion of the Mammalian Gene Collection (MGC)

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide

Detection of lineage-specific evolutionary changes among primate species

<p>Abstract</p> <p>Background</p> <p>Comparison of the human genome with other primates offers the opportunity to detect evolutionary events that created the diverse phenotypes among the primate species. Because the primate genomes are highly similar to one another, methods developed for analysis of more divergent species do not always detect signs of evolutionary selection.</p> <p>Results</p> <p>We have developed a new method, called DivE, specifically designed to find regions that have evolved either more or less rapidly than expected, for any clade within a set of very closely related species. Unlike some previous methods, DivE does not rely on rates of synonymous and nonsynonymous substitution, which enables it to detect evolutionary events in noncoding regions. We demonstrate using simulated data that DivE compares favorably to alternative methods, and we then apply DivE to the ENCODE regions in 14 primate species. We identify thousands of regions in these primates, ranging from 50 to >10000 bp in length, that appear to have experienced either constrained or accelerated rates of evolution. In particular, we detected 4942 regions that have potentially undergone positive selection in one or more primate species. Most of these regions occur outside of protein-coding genes, although we identified 20 proteins that have experienced positive selection.</p> <p>Conclusions</p> <p>DivE provides an easy-to-use method to predict both positive and negative selection in noncoding DNA, that is particularly well-suited to detecting lineage-specific selection in large genomes.</p

In vivo and in vitro synthesis of CM-proteins (A-hordeins) from barley (Hordeum vulgare L.)

CM-proteins from barley endosperm (CMa, CMb, CMc, CMd), which are the main components of the A-hordein fraction, are synthesized most actively 10 to 30 d after anthesis (maximum at 15–20 d). They are synthesized by membranebound polysomes as precursors of higher apparent molecular weight (13,000–21,000) than the mature proteins (12,000–16,000). The largest in vitro product (21,000) is the putative precursor of protein CMd (16,000), as it is selected with anti-CMd monospecific IgG's, and is coded by an mRNA of greater sedimentation coefficient (9 S) than those encoding the other three proteins (7.5 S). CM-proteins always appear in the soluble fraction, following different homogenization and subcellular fractionation procedures, indicating that these proteins are transferred to the soluble fraction after processing

Quantification of endogenous levels of IAA, IAAsp and IBA in micro-propagated shoots of hybrid chestnut pre-treated with IBA

Endogenous levels of indole-3-acetic acid (IAA), indole-3-acetylaspartic acid (IAAsp) and indole-3-butyric acid (IBA) were measured during the first 8 d of in vitro rooting of rootstock from the chestnut ‘M3’ hybrid by high performance liquid chromatography (HPLC). Rooting was induced either by dipping the basal ends of the shoots into a 4.92-mM IBA solution for 1 min or by sub-culturing the shoots on solid rooting medium supplemented with 14.8- μM IBA for 5 d. For root development, the induced shoots were transferred to auxin-free solid medium. Auxins were measured in the apical and basal parts of the shoots by means of HPLC. Endogenous levels of IAA and IAAsp were found to be greater in IBA-treated shoots than in control shoots. In extracts of the basal parts of the shoots, the concentration of free IAA showed a significant peak 2 d after either root inductive method and a subsequent gradual decrease for the remainder of the time course. The concentration of IAAsp peaked at day 6 in extracts of the basal parts of shoots induced with 14.8-μM IBA for 5 d, whereas shoots induced by dipping showed an initial increase until day 2 and then remained stable. In extracts from basal shoot portions induced by dipping, IBA concentration showed a transient peak at day 1 and a plateau between day 2 and 4, in contrast to the profile of shoots induced on auxin-containing medium, which showed a significant reduction between 4 and 6 d after transferred to auxin-free medium. All quantified auxins remained at a relatively low level, virtually constant, in extracts from apical shoot portions, as well as in extracts from control non-rooting shoots. In conclusion, the natural auxin IAA is the signal responsible for root induction, although it is driven by exogenous IBA independently of the adding conditions