Genome-wide association study in two cohorts from a multi-generational mouse advanced intercross line highlights the difficulty of replication due to study-specific heterogeneity

There has been extensive discussion of the Replication Crisis in many fields, including genome-wide association studies

Genome wide association analysis in a mouse advanced intercross line

We are grateful to Heather Lawson at Washington University in St. Louis for providing LG and SM genome sequences. We thank the Gilad Lab and Functional Genomics Facility at the University of Chicago for generating DNA- and RNA-seq data. We wish to acknowledge outstanding technical assistance from Apurva Chitre at UCSD and Mike Jarsulic at the Biological Sciences Division Center for Research Informatics at the University of Chicago. We thank Clarissa Parker, John Novembre, Graham McVicker, Joe Davis, Peter Carbonetto and Shyam Gopalakrishnan for advice, training, and mentorship. Our work was funded by NIDA (AAP: R01DA021336) and NIAMS (AL: R01AR056280). We received additional support from NIGMS (NMG: T32GM007197; MGD: T32GM07281), NIDA (NMG: F31DA03635803), NHGRI (MA: R01 HG002899), and the IMS Elphinstone Scholarship at the University of Aberdeen (AIHC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.Peer reviewedPublisher PD

Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2

Acknowledgements The authors would like to acknowledge Dr David A. Blizard for his role in the development of the ideas that led to this study and feedback on the manuscript, Professor Helen Macdonald for valuable advice on study design, Dr Leslie R. Noble for help with the UK Biobank data, and Dr Joseph P. Gyekis for help genotyping cohort 2 mice. The authors would like to acknowledge funding from the University of Aberdeen for the Maxwell computer cluster, the Elphinstone and IMS studentship for AIHC; a Schweppe Foundation Career Development Award (AAP), and the NIH (NIAMS (AL: R01AR056280) and NIDA (AAP:R01DA021336, AAP:R21DA024845, AAP:T32MH020065, NMG:F31DA03635803), NIGMS (NMG:T32GM007197), NHGRI (MA:R01HG002899))Peer reviewedPostprin

A Spectroscopic Study of a Large Sample of Wolf-Rayet Galaxies

We analyze long-slit spectral observations of 39 Wolf-Rayet (WR) galaxies with heavy element mass fraction ranging over 2 orders of magnitude, from Zsun/50 to 2Zsun. Nearly all galaxies in our sample show broad WR emission in the blue region of the spectrum (the blue bump) consisting of an unresolved blend of N III 4640, C III 4650, C IV 4658 and He II 4686 emission lines. Broad C IV 5808 emission (the red bump) is detected in 30 galaxies. Additionally, weaker WR emission lines are identified, most often the N III 4512 and Si III 4565 lines, which have very rarely or never been seen and discussed before in WR galaxies. These emission features are characteristic of WN7-WN8 and WN9-WN11 stars respectively. We derive the numbers of early WC (WCE) and late WN (WNL) stars from the luminosities of the red and blue bumps, and the number of O stars from the luminosity of the Hbeta emission line. Additionally, we propose a new technique for deriving the numbers of WNL stars from the N III 4512 and Si III 4565 emission lines. This technique is potentially more precise than the blue bump method because it does not suffer from contamination of WCE and early WN (WNE) stars and nebular gaseous emission. The N(WR)/N(O+WR) ratio decreases with decreasing metallicity, in agreement with predictions of evolutionary synthesis models. The N(WC)/N(WN) ratios and the equivalent widths of the blue bump EW(4650) and of the red bump EW(5808) derived from observations are also in satisfactory agreement with theoretical predictions.Comment: 49 pages, 9 figures, to appear in Astrophys.

Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies

Sprague Dawley (SD) rats are among the most widely used outbred laboratory rat populations. Despite this, the genetic characteristics of SD rats have not been clearly described, and SD rats are rarely used for experiments aimed at exploring genotype-phenotype relationships. In order to use SD rats to perform a genome-wide association study (GWAS), we collected behavioral data from 4,625 SD rats that were predominantly obtained from two commercial vendors, Charles River Laboratories and Harlan Sprague Dawley Inc. Using double-digest genotyping-by-sequencing (ddGBS), we obtained dense, high-quality genotypes at 291,438 SNPs across 4,061 rats. This genetic data allowed us to characterize the variation present in Charles River vs. Harlan SD rats. We found that the two populations are highly diverged (FST > 0.4). Furthermore, even for rats obtained from the same vendor, there was strong population structure across breeding facilities and even between rooms at the same facility. We performed multiple separate GWAS by fitting a linear mixed model that accounted for population structure and using meta-analysis to jointly analyze all cohorts. Our study examined Pavlovian conditioned approach (PavCA) behavior, which assesses the propensity for rats to attribute incentive salience to reward-associated cues. We identified 46 significant associations for the various metrics used to define PavCA. The surprising degree of population structure among SD rats from different sources has important implications for their use in both genetic and non-genetic studies

Genome wide association analysis in a mouse advanced intercross line

We are grateful to Heather Lawson at Washington University in St. Louis for providing LG and SM genome sequences. We thank the Gilad Lab and Functional Genomics Facility at the University of Chicago for generating DNA- and RNA-seq data. We wish to acknowledge outstanding technical assistance from Apurva Chitre at UCSD and Mike Jarsulic at the Biological Sciences Division Center for Research Informatics at the University of Chicago. We thank Clarissa Parker, John Novembre, Graham McVicker, Joe Davis, Peter Carbonetto and Shyam Gopalakrishnan for advice, training, and mentorship. Our work was funded by NIDA (AAP: R01DA021336) and NIAMS (AL: R01AR056280). We received additional support from NIGMS (NMG: T32GM007197; MGD: T32GM07281), NIDA (NMG: F31DA03635803), NHGRI (MA: R01 HG002899), and the IMS Elphinstone Scholarship at the University of Aberdeen (AIHC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.Peer reviewedPublisher PD

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

The Multiplanet System TOI-421: A Warm Neptune and a Super Puffy Mini-Neptune Transiting a G9 V Star in a Visual Binary

We report the discovery of a warm Neptune and a hot sub-Neptune transiting TOI-421 (BD-14 1137, TIC 94986319), a bright (V = 9.9) G9 dwarf star in a visual binary system observed by the Transiting Exoplanet Survey Satellite (TESS) space mission in Sectors 5 and 6. We performed ground-based follow-up observations—comprised of Las Cumbres Observatory Global Telescope transit photometry, NIRC2 adaptive optics imaging, and FIbre-fed Echellé Spectrograph, CORALIE, High Accuracy Radial velocity Planet Searcher, High Resolution Échelle Spectrometer, and Planet Finder Spectrograph high-precision Doppler measurements—and confirmed the planetary nature of the 16 day transiting candidate announced by the TESS team. We discovered an additional radial velocity signal with a period of five days induced by the presence of a second planet in the system, which we also found to transit its host star. We found that the inner mini-Neptune, TOI-421 b, has an orbital period of P_b = 5.19672 ± 0.00049 days, a mass of M_b = 7.17 ± 0.66 M⊕, and a radius of R_b = 2.68^(+0.19)_(-0.18) R⊕, whereas the outer warm Neptune, TOI-421 c, has a period of Pc = 16.06819 ± 0.00035 days, a mass of M_c = 16.42^(+1.06)_(-1.04) M⊕, a radius of R_c = 5.09^(+0.16)_(-0.15) R⊕ and a density of ρ_c = 0.685^(+0.080)_(-0.072) g cm⁻³. With its characteristics, the outer planet (ρ_c = 0.685^(+0.080)_(-0.072) g cm⁻³) is placed in the intriguing class of the super-puffy mini-Neptunes. TOI-421 b and TOI-421 c are found to be well-suited for atmospheric characterization. Our atmospheric simulations predict significant Lyα transit absorption, due to strong hydrogen escape in both planets, as well as the presence of detectable CH4 in the atmosphere of TOI-421 c if equilibrium chemistry is assumed