Framework for quantification of the dynamics of root colonization by pseudomonas fluorescens isolate SBW25

Colonization of the root surface, or rhizoplane, is one of the first steps for soil-borne bacteria to become established in the plant microbiome. However, the relative contributions of processes, such as bacterial attachment and proliferation is not well characterized, and this limits our ability to comprehend the complex dynamics of microbial communities in the rhizosphere. The work presented here addresses this knowledge gap. A model system was developed to acquire quantitative data on the colonization process of lettuce (Lactuca sativa L. cultivar. All Year Round) roots by Pseudomonas fluorescens isolate SBW25. A theoretical framework is proposed to calculate attachment rate and quantify the relative contribution of bacterial attachment to colonization. This allows the assessment of attachment rates on the root surface beyond the short time period during which it can be quantified experimentally. All techniques proposed are generic and similar analyses could be applied to study various combinations of plants and bacteria, or to assess competition between species. In the future this could allow for selection of microbial traits that improve early colonization and maintenance of targeted isolates in cropping systems, with potential applications for the development of biological fertilizers

Root architecture and rhizosphere–microbe interactions

Plant roots fulfil crucial tasks during a plant’s life. As roots encounter very diverse conditions while exploring the soil for resources, their growth and development must be responsive to changes in the rhizosphere, resulting in root architectures that are tailor-made for all prevailing circumstances. Using multi-disciplinary approaches, we are gaining more intricate insights into the regulatory mechanisms directing root system architecture. This Special Issue provides insights into our advancement of knowledge on different aspects of root development and identifies opportunities for future research

High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napusL.)

Background and Aims Root traits can be selected for crop improvement. Techniques such as soil excavations can be used to screen root traits in the field, but are limited to genotypes that are well-adapted to field conditions. The aim of this study was to compare a low-cost, high-throughput root phenotyping (HTP) technique in a controlled environment with field performance, using oilseed rape (OSR; Brassica napus) varieties. Methods Primary root length (PRL), lateral root length and lateral root density (LRD) were measured on 14-d-old seedlings of elite OSR varieties (n = 32) using a ‘pouch and wick’ HTP system (∼40 replicates). Six field experiments were conducted using the same varieties at two UK sites each year for 3 years. Plants were excavated at the 6- to 8-leaf stage for general vigour assessments of roots and shoots in all six experiments, and final seed yield was determined. Leaves were sampled for mineral composition from one of the field experiments. Key Results Seedling PRL in the HTP system correlated with seed yield in four out of six (r = 0·50, 0·50, 0·33, 0·49; P < 0·05) and with emergence in three out of five (r = 0·59, 0·22, 0·49; P < 0·05) field experiments. Seedling LRD correlated positively with leaf concentrations of some minerals, e.g. calcium (r = 0·46; P < 0·01) and zinc (r = 0·58; P < 0·001), but did not correlate with emergence, general early vigour or yield in the field. Conclusions Associations between PRL and field performance are generally related to early vigour. These root traits might therefore be of limited additional selection value, given that vigour can be measured easily on shoots/canopies. In contrast, LRD cannot be assessed easily in the field and, if LRD can improve nutrient uptake, then it may be possible to use HTP systems to screen this trait in both elite and more genetically diverse, non-field-adapted OSR

Ultracool dwarf benchmarks with \emph{Gaia} primaries

This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society. © 2017 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.We explore the potential of \emph{Gaia} for the field of benchmark ultracool/brown dwarf companions, and present the results of an initial search for metal-rich/metal-poor systems. A simulated population of resolved ultracool dwarf companions to \emph{Gaia} primary stars is generated and assessed. Of order $\sim$24,000 companions should be identifiable outside of the Galactic plane ($|b| > 10\,$deg) with large-scale ground- and space-based surveys including late M, L, T, and Y types. Our simulated companion parameter space covers $0.02 \le M/M_{\odot} \le 0.1$, $0.1 \le {\rm age/Gyr} \le 14$, and $-2.5 \le {\rm [Fe/H]} \le 0.5$, with systems required to have a false alarm probability $$0.6\, kau}\,Peer reviewedFinal Accepted Versio

Use of quercetin in animal feed : effects on the P-gp expression and pharmacokinetics of orally administrated enrofloxacin in chicken

Modulation of P-glycoprotein (P-gp, encoded by Mdr1) by xenobiotics plays central role in pharmacokinetics of various drugs. Quercetin has a potential to modulate P-gp in rodents, however, its effects on P-gp modulation in chicken are still unclear. Herein, study reports role of quercetin in modulation of P-gp expression and subsequent effects on the pharmacokinetics of enrofloxacin in broilers. Results show that P-gp expression was increased in a dose-dependent manner following exposure to quercetin in Caco-2 cells and tissues of chicken. Absorption rate constant and apparent permeability coefficient of rhodamine 123 were decreased, reflecting efflux function of P-gp in chicken intestine increased by quercetin. Quercetin altered pharmacokinetic of enrofloxacin by decreasing area under curve, peak concentration, and time to reach peak concentration and by increasing clearance rate. Molecular docking shows quercetin can form favorable interactions with binding pocket of chicken xenobiotic receptor (CXR). Results provide convincing evidence that quercetin induced P-gp expression in tissues by possible interaction with CXR, and consequently reducing bioavailability of orally administered enrofloxacin through restricting its intestinal absorption and liver/kidney clearance in broilers. The results can be further extended to guide reasonable use of quercetin to avoid drug-feed interaction occurred with co-administered enrofloxacin or other similar antimicrobials.Peer reviewedFinal Published versio

Spectrally-resolved UV photodesorption of CH4 in pure and layered ices

Context. Methane is among the main components of the ice mantles of insterstellar dust grains, where it is at the start of a rich solid-phase chemical network. Quantification of the photon-induced desorption yield of these frozen molecules and understanding of the underlying processes is necessary to accurately model the observations and the chemical evolution of various regions of the interstellar medium. Aims. This study aims at experimentally determining absolute photodesorption yields for the CH4 molecule as a function of photon energy. The influence of the ice composition is also investigated. By studying the methane desorption from layered CH4:CO ice, indirect desorption processes triggered by the excitation of the CO molecules is monitored and quantified. Methods. Tunable monochromatic VUV light from the DESIRS beamline of the SOLEIL synchrotron is used in the 7 - 13.6 eV (177 - 91 nm) range to irradiate pure CH4 or layers of CH4 deposited on top of CO ice samples. The release of species in the gas phase is monitored by quadrupole mass spectrometry and absolute photodesorption yields of intact CH4 are deduced. Results. CH4 photodesorbs for photon energies higher than ~9.1 eV (~136 nm). The photodesorption spectrum follows the absorption spectrum of CH4, which confirms a desorption mechanism mediated by electronic transitions in the ice. When it is deposited on top of CO, CH4 desorbs between 8 and 9 eV with a pattern characteristic of CO absorption, indicating desorption induced by energy transfer from CO molecules. Conclusions. The photodesorption of CH4 from the pure ice in various interstellar environments is around 2.0 x 10^-3 molecules per incident photon. Results on CO-induced indirect desorption of CH4 provide useful insights for the generalization of this process to other molecules co-existing with CO in ice mantles

Individual Dynamical Masses of Ultracool Dwarfs

We present the full results of our decade-long astrometric monitoring programs targeting 31 ultracool binaries with component spectral types M7-T5. Joint analysis of resolved imaging from Keck Observatory and Hubble Space Telescope and unresolved astrometry from CFHT/WIRCam yields parallactic distances for all systems, robust orbit determinations for 23 systems, and photocenter orbits for 19 systems. As a result, we measure 38 precise individual masses spanning 30-115 $M_{\rm Jup}$. We determine a model-independent substellar boundary that is $\approx$70 $M_{\rm Jup}$ in mass ($\approx$L4 in spectral type), and we validate Baraffe et al. (2015) evolutionary model predictions for the lithium-depletion boundary (60 $M_{\rm Jup}$ at field ages). Assuming each binary is coeval, we test models of the substellar mass-luminosity relation and find that in the L/T transition, only the Saumon & Marley (2008) "hybrid" models accounting for cloud clearing match our data. We derive a precise, mass-calibrated spectral type-effective temperature relation covering 1100-2800 K. Our masses enable a novel direct determination of the age distribution of field brown dwarfs spanning L4-T5 and 30-70 $M_{\rm Jup}$. We determine a median age of 1.3 Gyr, and our population synthesis modeling indicates our sample is consistent with a constant star formation history modulated by dynamical heating in the Galactic disk. We discover two triple-brown-dwarf systems, the first with directly measured masses and eccentricities. We examine the eccentricity distribution, carefully considering biases and completeness, and find that low-eccentricity orbits are significantly more common among ultracool binaries than solar-type binaries, possibly indicating the early influence of long-lived dissipative gas disks. Overall, this work represents a major advance in the empirical view of very low-mass stars and brown dwarfs.Comment: ApJS, in press. This arxiv posting contains all figures (111 pages) and tables (107 pages). Updated version contains additional acknowledgments and references and corrects typo

Orbital Architectures of Planet-Hosting Binaries:I. Forming Five Small Planets in the Truncated Disk of Kepler-444A

We present the first results from our Keck program investigating the orbital architectures of planet-hosting multiple star systems. Kepler-444 is a metal-poor triple star system that hosts five sub-Earth-sized planets orbiting the primary star (Kepler-444A), as well as a spatially unresolved pair of M dwarfs (Kepler-444BC) at a projected distance of 1.8" (66 AU). We combine our Keck/NIRC2 adaptive optics astrometry with multi-epoch Keck/HIRES RVs of all three stars to determine a precise orbit for the BC pair around A, given their empirically constrained masses. We measure minimal astrometric motion ($1.0\pm0.6$ mas yr$^{-1}$, or $0.17\pm0.10$ km s$^{-1}$), but our RVs reveal significant orbital velocity ($1.7\pm0.2$ km s$^{-1}$) and acceleration ($7.8\pm0.5$ m s$^{-1}$ yr$^{-1}$). We determine a highly eccentric stellar orbit ($e=0.864\pm0.023$) that brings the tight M dwarf pair within $5.0^{+0.9}_{-1.0}$ AU of the planetary system. We validate that the system is dynamically stable in its present configuration via n-body simulations. We find that the A$-$BC orbit and planetary orbits are likely aligned (98%) given that they both have edge-on orbits and misalignment induces precession of the planets out of transit. We conclude that the stars were likely on their current orbits during the epoch of planet formation, truncating the protoplanetary disk at $\approx$2 AU. This truncated disk would have been severely depleted of solid material from which to form the total $\approx$1.5 $M_{\rm Earth}$ of planets. We thereby strongly constrain the efficiency of the conversion of dust into planets and suggest that the Kepler-444 system is consistent with models that explain the formation of more typical close-in Kepler planets in normal, not truncated, disks.Comment: accepted to Ap

PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice

DNA transposon piggyBac (PB) is a newly established mutagen for large-scale mutagenesis in mice. We have designed and implemented an integrated database system called PBmice (PB Mutagenesis Information CEnter) for storing, retrieving and displaying the information derived from PB insertions (INSERTs) in the mouse genome. This system is centered on INSERTs with information including their genomic locations and flanking genomic sequences, the expression levels of the hit genes, and the expression patterns of the trapped genes if a trapping vector was used. It also archives mouse phenotyping data linked to INSERTs, and allows users to conduct quick and advanced searches for genotypic and phenotypic information relevant to a particular or a set of INSERT(s). Sequence-based information can be cross-referenced with other genomic databases such as Ensembl, BLAST and GBrowse tools used in PBmice offer enhanced search and display for additional information relevant to INSERTs. The total number and genomic distribution of PB INSERTs, as well as the availability of each PB insertional LINE can also be viewed with user-friendly interfaces. PBmice is freely available at http://www.idmshanghai.cn/PBmice or http://www.scbit.org/PBmice/