Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence

Universally Sloppy Parameter Sensitivities in Systems Biology

Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring \emph{in vivo} biochemical parameters is difficult, and collectively fitting them to other data often yields large parameter uncertainties. Nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. We also showed that the model had a `sloppy' spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. Here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. Strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. We also test several consequences of this sloppiness for building predictive models. In particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. Tests over our model collection are consistent with this suggestion. This difficulty with collective fits may seem to argue for direct parameter measurements, but sloppiness also implies that such measurements must be formidably precise and complete to usefully constrain many model predictions. We confirm this implication in our signaling model. Our results suggest that sloppy sensitivity spectra are universal in systems biology models. The prevalence of sloppiness highlights the power of collective fits and suggests that modelers should focus on predictions rather than on parameters.Comment: Submitted to PLoS Computational Biology. Supplementary Information available in "Other Formats" bundle. Discussion slightly revised to add historical contex

An ALMA Constraint on the GSC 6214-210 B Circum-Substellar Accretion Disk Mass

We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of GSC 6214-210 A and B, a solar-mass member of the 5-10 Myr Upper Scorpius association with a 15 $\pm$ 2 Mjup companion orbiting at $\approx$330 AU (2.2"). Previous photometry and spectroscopy spanning 0.3-5 $\mu$m revealed optical and thermal excess as well as strong H$\alpha$ and Pa~$\beta$ emission originating from a circum-substellar accretion disk around GSC 6214-210 B, making it the lowest mass companion with unambiguous evidence of a subdisk. Despite ALMA's unprecedented sensitivity and angular resolution, neither component was detected in our 880 $\mu$m (341 GHz) continuum observations down to a 3-$\sigma$ limit of 0.22 mJy/beam. The corresponding constraints on the dust mass and total mass are <0.15 Mearth and <0.05 Mjup, respectively, or <0.003% and <0.3% of the mass of GSC 6214-210 B itself assuming a 100:1 gas-to-dust ratio and characteristic dust temperature of 10-20 K. If the host star possesses a putative circum-stellar disk then at most it is a meager 0.0015% of the primary mass, implying that giant planet formation has certainly ceased in this system. Considering these limits and its current accretion rate, GSC 6214-210 B appears to be at the end stages of assembly and is not expected to gain any appreciable mass over the next few Myr.Comment: Accepted to ApJ

Signs of Binary Evolution in 7 Magnetic DA White Dwarfs

We present our findings on the spectral analysis of seven magnetic white dwarfs that were presumed to be double degenerates. We obtained time-resolved spectroscopy at the Gemini Observatory to look for evidence of binarity or fast rotation. We find three of our targets have rotation periods of less than an hour based on the shifting positions of the Zeeman-split H$\alpha$ components: 13, 35, and 39 min, and we find one more target with a ~hour long period that is currently unconstrained. We use offset dipole models to determine the inclination, magnetic field strength, and dipole offset of each target. The average surface field strengths of our fast rotators vary by 1-2 MG between different spectra. In all cases, the observed absorption features are too shallow compared to our models. This could be due to extra flux from a companion for our three low-mass targets, but the majority of our sample likely requires an inhomogeneous surface composition. Including an additional magnetic white dwarf with similar properties presented in the literature, we find that 5 of the 8 targets in this sample show field variations on minute/hour timescales. A crystallization driven dynamo can potentially explain the magnetic fields in three of our targets with masses above $0.7~M_{\odot}$ but another mechanism is still needed to explain their rapid rotation. We suggest that rapid rotation or low-masses point to binary evolution as the likely source of magnetism in 7 of these 8 targets.Comment: 13 pages, 14 figures, accepted for publication in MNRA

Hydrogen Balmer Line Broadening in Solar and Stellar Flares

The broadening of the hydrogen lines during flares is thought to result from increased charge (electron, proton) density in the flare chromosphere. However, disagreements between theory and modeling prescriptions have precluded an accurate diagnostic of the degree of ionization and compression resulting from flare heating in the chromosphere. To resolve this issue, we have incorporated the unified theory of electric pressure broadening of the hydrogen lines into the non-LTE radiative transfer code RH. This broadening prescription produces a much more realistic spectrum of the quiescent, A0 star Vega compared to the analytic approximations used as a damping parameter in the Voigt profiles. We test recent radiative-hydrodynamic (RHD) simulations of the atmospheric response to high nonthermal electron beam fluxes with the new broadening prescription and find that the Balmer lines are over-broadened at the densest times in the simulations. Adding many simultaneously heated and cooling model loops as a "multithread" model improves the agreement with the observations. We revisit the three-component phenomenological flare model of the YZ CMi Megaflare using recent and new RHD models. The evolution of the broadening, line flux ratios, and continuum flux ratios are well-reproduced by a multithread model with high-flux nonthermal electron beam heating, an extended decay phase model, and a "hot spot" atmosphere heated by an ultrarelativistic electron beam with reasonable filling factors: 0.1%, 1%, and 0.1% of the visible stellar hemisphere, respectively. The new modeling motivates future work to understand the origin of the extended gradual phase emission.Comment: 31 pages, 13 figures, 2 tables, accepted for publication in the Astrophysical Journa

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.

The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45

Principal Response Curve Analysis of Arthropod Community Abundance Data with Sparse Subsets

Principal response curve (PRC) analysis was applied to an assessment of the ecological impact of the genetically-modified (GM), insect-resistant, cotton MON 88702 on predatory Hemiptera communities in the field. The field community was represented by ten taxa collected ten times across the season at six sites, in which individual taxa were not observed in at least 25% of the time (unique site x collection combinations). These complete absences and those nearly so, called sparse subsets of the data in this investigation, were the result of geoclimatic and seasonal variations, which are both independent of the treatment effect for which the PRC analysis is intended. If the sparse subsets were included in the analysis, the treatment effect would be underestimated. Here, a modified analysis is proposed to remove those sparse subsets and to be performed on the incomplete data. In the application to MON 88702, four components (PRC1-4) were significant at the 5% level by the modified method, when more than 50% of the data were excluded due to no- or low responses, and five (PRC1-5) by the classical method. While PRC1-2 was highly consistent between two methods, PRC3-5 was largely different because of sparse subsets of the data. Differences in results between two methods demonstrate that excluding sparse subsets prevented the bias in the estimation of the treatment effect and the relationship with the community from confounding with the environmental variation that caused the sparse data. In this regard, the modification should be considered as a supplement of the classical PRC analysis and recommended when abundance data have sparse subsets

Hubble Space Telescope NICMOS Observations of T Dwarfs: Brown Dwarf Multiplicity and New Probes of the L/T Transition

We present the results of a Hubble Space Telescope NICMOS imaging survey of 22 T-type field brown dwarfs. Five are resolved as binary systems with angular separations of 0"05-0"35, and companionship is established on the basis of component F110W-F170M colors (indicative of CH4 absorption) and low probabilities of background contamination. Prior ground-based observations show 2MASS 1553+1532AB to be a common proper motion binary. The properties of these systems - low multiplicity fraction (11[+7][-3]% resolved, as corrected for sample selection baises), close projected separations (a = 1.8-5.0 AU) and near-unity mass ratios - are consistent with previous results for field brown dwarf binaries. Three of the binaries have components that span the poorly-understood transition between L dwarfs and T dwarfs. Spectral decomposition analysis of one of these, SDSS 1021-0304AB, reveals a peculiar flux reversal between its components, as its T5 secondary is ~30% brighter at 1.05 and 1.27 micron than its T1 primary. This system, 2MASS 0518-2828AB and SDSS 1534+1615AB all demonstrate that the J-band brightening observed between late-type L to mid-type T dwarfs is an intrinsic feature of this spectral transition, albeit less pronounced than previously surmised. We also find that the resolved binary fraction of L7 to T3.5 dwarfs is twice that of other L and T dwarfs, an anomaly that can be explained by a relatively rapid evolution of brown dwarfs through the L/T transition, perhaps driven by dynamic (nonequilibrium) depletion of photospheric condensates.Comment: ~40 pages, 17 figures, accepted for publication to ApJ. Note that emulateapj style file cuts off part of Table

Atomic hydrogen in IllustrisTNG galaxies: the impact of environment parallelled with local 21-cm surveys

We investigate the influence of environment on the cold-gas properties of galaxies at z=0 within the TNG100 cosmological, magnetohydrodynamic simulation, part of the IllustrisTNG suite. We extend previous post-processing methods for breaking gas cells into their atomic and molecular phases, and build detailed mocks to comprehensively compare to the latest surveys of atomic hydrogen (HI) in nearby galaxies, namely ALFALFA and xGASS. We use TNG100 to explore the HI content, star formation activity, and angular momentum of satellite galaxies, each as a function of environment, and find that satellites are typically a factor of ~3 poorer in HI than centrals of the same stellar mass, with the exact offset depending sensitively on parent halo mass. Due to the large physical scales on which HI measurements are made (~45--245 kpc), contributions from gas not bound to the galaxy of interest but in the same line of sight crucially lead to larger HI mass measurements in the mocks in many cases, ultimately aligning with observations. This effect is mass-dependent and naturally greater for satellites than centrals, as satellites are never isolated by definition. We also show that HI stripping in TNG100 satellites is closely accompanied by quenching, in tension with observational data that instead favour that HI is preferentially stripped before star formation is reduced.Comment: Published in MNRAS. Main body (full paper): 18 (22) pages, 10 (11) figures. New-found bug introduced in v4 mock plots fixed. BaryMP issue fixed per footnote in Dave et al. (2020). All changes are minor and do not affect text or conclusion