Early selection of novel triploid hybrids of shrub willow with improved biomass yield relative to diploids

BACKGROUND: Genetic improvement of shrub willow (Salix), a perennial energy crop common to temperate climates, has led to the development of new cultivars with improved biomass yield, pest and disease resistance, and biomass composition suitable for bioenergy applications. These improvements have largely been associated with species hybridization, yet little is known about the genetic mechanisms responsible for improved yield and performance of certain willow species hybrids. RESULTS: The top performing genotypes in this study, representing advanced pedigrees compared with those in previous studies, were mostly triploid in nature and outperformed current commercial cultivars. Of the genotypes studied, the diploids had the lowest mean yield of 8.29 oven dry Mg ha(−1) yr(−1), while triploids yielded 12.65 Mg ha(−1) yr(−1), with the top five producing over 16 Mg ha(−1) yr(−1). Triploids had high stem area and height across all three years of growth in addition to greatest specific gravity. The lowest specific gravity was observed among the tetraploid genotypes. Height was the early trait most correlated with and the best predictor of third-year yield. CONCLUSIONS: These results establish a paradigm for future breeding and improvement of Salix bioenergy crops based on the development of triploid species hybrids. Stem height and total stem area are effective traits for early prediction of relative yield performance

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).

Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region. We demonstrate that Salix purpurea also has a ZW system on chromosome 15. The sex determination region has reduced recombination, high structural polymorphism, an abundance of transposable elements, and contains genes that are involved in sex expression in other plants. We also show that chromosome 19 contains sex-associated markers in this S. purpurea assembly, along with other autosomes. This raises the intriguing possibility of a translocation of the sex determination region within the Salicaceae lineage, suggesting a common evolutionary origin of the Populus and Salix sex determination loci

Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality

BACKGROUND: There is currently considerable interest in developing renewable sources of energy. One strategy is the biological conversion of plant biomass to liquid transportation fuel. Several technical hurdles impinge upon the economic feasibility of this strategy, including the development of energy crops amenable to facile deconstruction. Reliable assays to characterize feedstock quality are needed to measure the effects of pre-treatment and processing and of the plant and microbial genetic diversity that influence bioconversion efficiency. RESULTS: We used the anaerobic bacterium Clostridium phytofermentans to develop a robust assay for biomass digestibility and conversion to biofuels. The assay utilizes the ability of the microbe to convert biomass directly into ethanol with little or no pre-treatment. Plant samples were added to an anaerobic minimal medium and inoculated with C. phytofermentans, incubated for 3 days, after which the culture supernatant was analyzed for ethanol concentration. The assay detected significant differences in the supernatant ethanol from wildtype sorghum compared with brown midrib sorghum mutants previously shown to be highly digestible. Compositional analysis of the biomass before and after inoculation suggested that differences in xylan metabolism were partly responsible for the differences in ethanol yields. Additionally, we characterized the natural genetic variation for conversion efficiency in Brachypodium distachyon and shrub willow (Salix spp.). CONCLUSION: Our results agree with those from previous studies of lignin mutants using enzymatic saccharification-based approaches. However, the use of C. phytofermentans takes into consideration specific organismal interactions, which will be crucial for simultaneous saccharification fermentation or consolidated bioprocessing. The ability to detect such phenotypic variation facilitates the genetic analysis of mechanisms underlying plant feedstock quality

A new benchmark T8-9 brown dwarf and a couple of new mid-T dwarfs from the UKIDSS DR5+ LAS

Benchmark brown dwarfs are those objects for which fiducial constraints are available, including effective temperature, parallax, age, metallicity. We searched for new cool brown dwarfs in 186 sq.deg. of the new area covered by the data release DR5+ of the UKIDSS Large Area Survey. Follow-up optical and near-infrared broad-band photometry, and methane imaging of four promising candidates, revealed three objects with distinct methane absorption, typical of mid- to late-T dwarfs, and one possibly T4 dwarf. The latest-type object, classified as T8-9, shares its large proper motion with Ross 458 (BD+13o2618), an active M0.5 binary which is 102" away, forming a hierarchical low-mass star+brown dwarf system. Ross 458C has an absolute J-band magnitude of 16.4, and seems overluminous, particularly in the K band, compared to similar field brown dwarfs. We estimate the age of the system to be less than 1 Gyr, and its mass to be as low as 14 Jupiter masses for the age of 1 Gyr. At 11.4 pc, this new late T benchmark dwarf is a promising target to constrain the evolutionary and atmospheric models of very low-mass brown dwarfs. We present proper motion measurements for our targets and for 13 known brown dwarfs. Two brown dwarfs have velocities typical of the thick disk and may be old brown dwarfs.Comment: 15 pages, 10 figures and 6 tables. Accepted by MNRAS. Uses mn2e.cls and aas_macr

Primeval very low-mass stars and brown dwarfs - III. The halo transitional brown dwarfs

This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society. © 2018 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.We report the discovery of an esdL3 subdwarf, ULAS J020858.62+020657.0 and a usdL4.5 subdwarf, ULAS J230711.01+014447.1. They were identified as L subdwarfs by optical spectra obtained with the Gran Telescopio Canarias, and followed up by optical to near infrared spectroscopy with the Very Large Telescope. We also obtained an optical to near infrared spectrum of a previously known L subdwarf, ULAS J135058.85+081506.8, and re-classified it as a usdL3 subdwarf. These three objects all have typical halo kinematics. They have $T_{\rm eff}$ around 2050-2250 K, $-$1.8 $\leq$ [Fe/H] $\leq -$1.5, and mass around 0.0822-0.0833 M$_{\odot}$, according to model spectral fitting and evolutionary models. These sources are likely halo transitional brown dwarfs with unsteady hydrogen fusions, as their masses are just below the hydrogen-burning minimum mass, which is $\sim$ 0.0845 M$_{\odot}$ at [Fe/H] = $-$1.6 and $\sim$ 0.0855 M$_{\odot}$ at [Fe/H] = $-$1.8. Including these, there are now nine objects in the `halo brown dwarf transition zone', which is a `substellar subdwarf gap' spans a wide temperature range within a narrow mass range of the substellar population.Peer reviewedFinal Accepted Versio

A spectroscopic and proper motion search of Sloan Digital Sky Survey : red subdwarfs in binary systems

Red subdwarfs in binary systems are crucial for both model calibration and spectral classification. We search for red subdwarfs in binary systems from a sample of high proper motion objects with Sloan Digital Sky Survey spectroscopy. We present here discoveries from this search, as well as highlight several additional objects of interest. We find 30 red subdwarfs in wide binary systems including: two with spectral type of esdM5.5, 6 companions to white dwarfs and 3 carbon-enhanced red subdwarfs with normal red subdwarf companions. 15 red subdwarfs in our sample are partially resolved close binary systems. With this binary sample, we estimate the low limit of the red subdwarf binary fraction of similar to 10 per cent. We find that the binary fraction goes down with decreasing masses and metallicities of red subdwarfs. A spectroscopic esdK7 subdwarf + white dwarf binary candidate is also reported. 30 new M subdwarfs have spectral type of >= M6 in our sample. We also derive relationships between spectral types and absolute magnitudes in the optical and near-infrared for M and L subdwarfs, and we present an M subdwarf sample with measured U, V, W space velocities.Peer reviewe

A 1500 deg2 near infrared proper motion catalogue from the UKIDSS Large Area Survey

The United Kingdom Infrared Deep Sky Survey (UKIDSS) Large Area Survey (LAS) began in 2005, with the start of the UKIDSS programme as a 7 year effort to survey roughly 4000 deg2 at high Galactic latitudes in Y, J, H and K bands. The survey also included a significant quantity of two epoch J band observations, with an epoch baseline greater than 2 years to calculate proper motions. We present a near-infrared proper motion catalogue for the 1500 deg2 of the two epoch LAS data, which includes 135 625 stellar sources and a further 88 324 with ambiguous morphological classifications, all with motions detected above the 5σ level. We developed a custom proper motion pipeline which we describe here. Our catalogue agrees well with the proper motion data supplied for a 300 deg2 subset in the current Wide Field Camera Science Archive (WSA) 10th data release (DR10) catalogue, and in various optical catalogues, but it benefits from a larger matching radius and hence a larger upper proper motion detection limit. We provide absolute proper motions, using LAS galaxies for the relative to absolute correction. By using local second-order polynomial transformations, as opposed to linear transformations in the WSA, we correct better for any local distortions in the focal plane, not including the radial distortion that is removed by the UKIDSS pipeline. We present the results of proper motion searches for new brown dwarfs and white dwarfs. We discuss 41 sources in the WSA DR10 overlap with our catalogue with proper motions >300 mas yr−1, several of which are new detections. We present 15 new candidate ultracool dwarf binary systems

A large spectroscopic sample of L and T dwarfs from UKIDSS LAS : peculiar objects, binaries, and space density

This is a pre-copyedited, author-produced PDF of an article accepted for publication in Monthly Notices of the Royal Astronomical Society following peer review. The version of record [F. Marocco, et al, 'A large spectroscopic sample of L and T dwarfs from UKIDSS LAS: peculiar objects, binaries, and space density', MNRAS, Vol. 449)4): 3651-3692, April 2015] is available online at: https://doi.org/10.1093/mnras/stv530.We present the spectroscopic analysis of a large sample of late-M, L, and T dwarfs from UKIDSS. Using the YJHK photometry from ULAS and the red-optical photometry from SDSS we selected a sample of 262 brown dwarf candidates and we followed-up 196 of them using X-shooter on the VLT. The large wavelength coverage (0.30-2.48 $\mu$m) and moderate resolution (R~5000-9000) of X-shooter allowed us to identify peculiar objects including 22 blue L dwarfs, 2 blue T dwarfs, and 2 low gravity M dwarfs. Using a spectral indices-based technique we identified 27 unresolved binary candidates, for which we determined the spectral type of the potential components via spectral deconvolution. The spectra allowed us to measure the equivalent width of the prominent absorption features and to compare them to atmospheric models. Cross-correlating the spectra with a radial velocity standard, we measured the radial velocity for our targets, and we determined the distribution of the sample, which is centred at -1.7$\pm$1.2 km s$^{-1}$ with a dispersion of 31.5 km s$^{-1}$. Using our results we estimated the space density of field brown dwarfs and compared it with the results of numerical simulations. Depending on the binary fraction, we found that there are (0.85$\pm$0.55) x 10$^{-3}$ to (1.00$\pm$0.64) x 10$^{-3}$ objects per cubic parsec in the L4-L6.5 range, (0.73$\pm$0.47) x 10$^{-3}$ to (0.85$\pm$0.55) x 10$^{-3}$ objects per cubic parsec in the L7-T0.5 range, and (0.74$\pm$0.48) x 10$^{-3}$ to (0.88$\pm$0.56) x 10$^{-3}$ objects per cubic parsec in the T1-T4.5 range. There seem to be an excess of objects in the L/T transition with respect to the late T dwarfs, a discrepancy that could be explained assuming a higher binary fraction than expected for the L/T transition, or that objects in the high-mass end and low-mass end of this regime form in different environments, i.e. following different IMFs.Peer reviewe

49 new T dwarfs identified using methane imaging

We present the discovery of 49 new photometrically classified T dwarfs from the combination of large infrared and optical surveys combined with follow-up TNG photometry. We used multi-band infrared and optical photometry from the UKIRT and Sloan Digital Sky Surveys to identify possible brown dwarf candidates, which were then confirmed using methane filter photometry. We have defined a new photometric conversion between CH4s - CH4l colour and spectral type for T4 to T8 brown dwarfs based on a part of the sample that has been followed up using methane photometry and spectroscopy. Using methane differential photometry as a proxy for spectral type for T dwarfs has proved to be a very efficient technique. Of a subset of 45 methane selected brown dwarfs that were observed spectroscopically, 100% were confirmed as T dwarfs. Future deep imaging surveys will produce large samples of faint brown dwarf candidates, for which spectroscopy will not be feasible. When broad wavelength coverage is unavailable, methane imaging offers a means to efficiently classify candidates from such surveys using just a pair of near-infrared images.Peer reviewe

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London