Complete Genome Sequences of Paenibacillus Larvae Phages BN12, Dragolir, Kiel007, Leyra, Likha, Pagassa, PBL1c, and Tadhana

We present here the complete genomes of eight phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA

TESS spots a mini-neptune interior to a hot saturn in the TOI-2000 system

Hot jupiters (P 60 $\mathrm{M}_\oplus$) are almost always found alone around their stars, but four out of hundreds known have inner companion planets. These rare companions allow us to constrain the hot jupiter's formation history by ruling out high-eccentricity tidal migration. Less is known about inner companions to hot Saturn-mass planets. We report here the discovery of the TOI-2000 system, which features a hot Saturn-mass planet with a smaller inner companion. The mini-neptune TOI-2000 b ($2.70 \pm 0.15 \,\mathrm{R}_\oplus$, $11.0 \pm 2.4 \,\mathrm{M}_\oplus$) is in a 3.10-day orbit, and the hot saturn TOI-2000 c ($8.14^{+0.31}_{-0.30} \,\mathrm{R}_\oplus$, $81.7^{+4.7}_{-4.6} \,\mathrm{M}_\oplus$) is in a 9.13-day orbit. Both planets transit their host star TOI-2000 (TIC 371188886, V = 10.98, TESS magnitude = 10.36), a metal-rich ([Fe/H] = $0.439^{+0.041}_{-0.043}$) G dwarf 174 pc away. TESS observed the two planets in sectors 9-11 and 36-38, and we followed up with ground-based photometry, spectroscopy, and speckle imaging. Radial velocities from CHIRON, FEROS, and HARPS allowed us to confirm both planets by direct mass measurement. In addition, we demonstrate constraining planetary and stellar parameters with MIST stellar evolutionary tracks through Hamiltonian Monte Carlo under the PyMC framework, achieving higher sampling efficiency and shorter run time compared to traditional Markov chain Monte Carlo. Having the brightest host star in the V band among similar systems, TOI-2000 b and c are superb candidates for atmospheric characterization by the JWST, which can potentially distinguish whether they formed together or TOI-2000 c swept along material during migration to form TOI-2000 b.Comment: v3 adds RV frequency analysis; 25 pages, 11 figures, 14 tables; revision submitted to MNRAS; machine-readable tables available as ancillary files; posterior samples available from Zenodo at https://doi.org/10.5281/zenodo.7683293 and source code at https://doi.org/10.5281/zenodo.798826

The TESS Grand Unified Hot Jupiter Survey. II. Twenty New Giant Planets

NASA's Transiting Exoplanet Survey Satellite (TESS) mission promises to improve our understanding of hot Jupiters by providing an all-sky, magnitude-limited sample of transiting hot Jupiters suitable for population studies. Assembling such a sample requires confirming hundreds of planet candidates with additional follow-up observations. Here, we present twenty hot Jupiters that were detected using TESS data and confirmed to be planets through photometric, spectroscopic, and imaging observations coordinated by the TESS Follow-up Observing Program (TFOP). These twenty planets have orbital periods shorter than 7 days and orbit relatively bright FGK stars ($10.9 < G < 13.0$). Most of the planets are comparable in mass to Jupiter, although there are four planets with masses less than that of Saturn. TOI-3976 b, the longest period planet in our sample ($P = 6.6$ days), may be on a moderately eccentric orbit ($e = 0.18\pm0.06$), while observations of the other targets are consistent with them being on circular orbits. We measured the projected stellar obliquity of TOI-1937A b, a hot Jupiter on a 22.4 hour orbit with the Rossiter-McLaughlin effect, finding the planet's orbit to be well-aligned with the stellar spin axis ($|\lambda| = 4.0\pm3.5^\circ$). We also investigated the possibility that TOI-1937 is a member of the NGC 2516 open cluster, but ultimately found the evidence for cluster membership to be ambiguous. These objects are part of a larger effort to build a complete sample of hot Jupiters to be used for future demographic and detailed characterization work.Comment: 67 pages, 11 tables, 13 figures, 2 figure sets. Resubmitted to ApJS after revision

Biomass preservation in impact melt ejecta

Meteorites can have played a role in the delivery of the building blocks of life to Earth only if organic compounds are able to survive the high pressures and temperatures of an impact event. Although experimental impact studies have reported the survival of organic compounds, there are uncertainties in scaling experimental conditions to those of a meteorite impact on Earth and organic matter has not been found in highly shocked impact materials in a natural setting. Impact glass linked to the 1.2-km-diameter Darwin crater in western Tasmania is strewn over an area exceeding 400 km2 and is thought to have been ejected by a meteorite impact about 800 kyr ago into terrain consisting of rainforest and swamp. Here we use pyrolysis–gas chromatography–mass spectrometry to show that biomarkers representative of plant species in the local ecosystem—including cellulose, lignin, aliphatic biopolymer and protein remnants—survived the Darwin impact. We find that inside the impact glass the organic components are trapped in porous carbon spheres. We propose that the organic material was captured within impact melt and preserved when the melt quenched to glass, preventing organic decomposition since the impact. We suggest that organic material can survive capture and transport in products of extreme impact processing, at least for a Darwin-sized impact event

Large-scale meta-genome-wide association study reveals common genetic factors linked to radiation-induced acute toxicities across cancer types.

Acknowledgements: The study sponsors were not involved in the design of the study; the collection, analysis, and interpretation of the data; the writing of the manuscript; or the decision to submit the manuscript for publication. We thank all patients who participated in the study and the participating clinic staff for their contribution to data collection. This publication presents data from the Head and Neck 5000 study. The study was a component of independent research funded by the NIHR under its Programme Grants for Applied Research scheme (RP-PG-0707-10034). The views expressed in this publication are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health. Core funding was also provided through awards from Above and Beyond, University Hospitals Bristol and Weston Research Capability Funding, and the NIHR Senior Investigator award to Professor Andy Ness. Genotyping was funded by World Cancer Research Fund Pilot Grant (grant No. 2018/1792), Above and Beyond, Wellcome Trust Research Training Fellowship (201237/Z/16/Z), and Cancer Research UK Cancer Research UK Programme Grant, the Integrative Cancer Epidemiology Programme (grant No. C18281/A19169). The VHIO authors acknowledge the Cellex Foundation for providing research equipment and facilities and thank CERCA Program/Generalitat de Catalunya for institutional support.Funder: National Institute for Health Research; DOI: https://doi.org/10.13039/501100000272Funder: The Taylor Family FoundationFunder: Cancer Research UK; DOI: https://doi.org/10.13039/501100000289Funder: National Medical Research Council; DOI: https://doi.org/10.13039/501100001349BACKGROUND: This study was designed to identify common genetic susceptibility and shared genetic variants associated with acute radiation-induced toxicity across 4 cancer types (prostate, head and neck, breast, and lung). METHODS: A genome-wide association study meta-analysis was performed using 19 cohorts totaling 12 042 patients. Acute standardized total average toxicity (STATacute) was modelled using a generalized linear regression model for additive effect of genetic variants, adjusted for demographic and clinical covariates (rSTATacute). Linkage disequilibrium score regression estimated shared single-nucleotide variation (SNV-formerly SNP)-based heritability of rSTATacute in all patients and for each cancer type. RESULTS: Shared SNV-based heritability of STATacute among all cancer types was estimated at 10% (SE = 0.02) and was higher for prostate (17%, SE = 0.07), head and neck (27%, SE = 0.09), and breast (16%, SE = 0.09) cancers. We identified 130 suggestive associated SNVs with rSTATacute (5.0 × 10‒8 < P < 1.0 × 10‒5) across 25 genomic regions. rs142667902 showed the strongest association (effect allele A; effect size ‒0.17; P = 1.7 × 10‒7), which is located near DPPA4, encoding a protein involved in pluripotency in stem cells, which are essential for repair of radiation-induced tissue injury. Gene-set enrichment analysis identified 'RNA splicing via endonucleolytic cleavage and ligation' (P = 5.1 × 10‒6, P = .079 corrected) as the top gene set associated with rSTATacute among all patients. In silico gene expression analysis showed that the genes associated with rSTATacute were statistically significantly up-regulated in skin (not sun exposed P = .004 corrected; sun exposed P = .026 corrected). CONCLUSIONS: There is shared SNV-based heritability for acute radiation-induced toxicity across and within individual cancer sites. Future meta-genome-wide association studies among large radiation therapy patient cohorts are worthwhile to identify the common causal variants for acute radiotoxicity across cancer types

Large-scale meta-genome-wide association study reveals common genetic factors linked to radiation-induced acute toxicities across cancer types.

Acknowledgements: The study sponsors were not involved in the design of the study; the collection, analysis, and interpretation of the data; the writing of the manuscript; or the decision to submit the manuscript for publication. We thank all patients who participated in the study and the participating clinic staff for their contribution to data collection. This publication presents data from the Head and Neck 5000 study. The study was a component of independent research funded by the NIHR under its Programme Grants for Applied Research scheme (RP-PG-0707-10034). The views expressed in this publication are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health. Core funding was also provided through awards from Above and Beyond, University Hospitals Bristol and Weston Research Capability Funding, and the NIHR Senior Investigator award to Professor Andy Ness. Genotyping was funded by World Cancer Research Fund Pilot Grant (grant No. 2018/1792), Above and Beyond, Wellcome Trust Research Training Fellowship (201237/Z/16/Z), and Cancer Research UK Cancer Research UK Programme Grant, the Integrative Cancer Epidemiology Programme (grant No. C18281/A19169). The VHIO authors acknowledge the Cellex Foundation for providing research equipment and facilities and thank CERCA Program/Generalitat de Catalunya for institutional support.Funder: National Institute for Health Research; DOI: https://doi.org/10.13039/501100000272Funder: The Taylor Family FoundationFunder: Cancer Research UK; DOI: https://doi.org/10.13039/501100000289Funder: National Medical Research Council; DOI: https://doi.org/10.13039/501100001349BACKGROUND: This study was designed to identify common genetic susceptibility and shared genetic variants associated with acute radiation-induced toxicity across 4 cancer types (prostate, head and neck, breast, and lung). METHODS: A genome-wide association study meta-analysis was performed using 19 cohorts totaling 12 042 patients. Acute standardized total average toxicity (STATacute) was modelled using a generalized linear regression model for additive effect of genetic variants, adjusted for demographic and clinical covariates (rSTATacute). Linkage disequilibrium score regression estimated shared single-nucleotide variation (SNV-formerly SNP)-based heritability of rSTATacute in all patients and for each cancer type. RESULTS: Shared SNV-based heritability of STATacute among all cancer types was estimated at 10% (SE = 0.02) and was higher for prostate (17%, SE = 0.07), head and neck (27%, SE = 0.09), and breast (16%, SE = 0.09) cancers. We identified 130 suggestive associated SNVs with rSTATacute (5.0 × 10‒8 < P < 1.0 × 10‒5) across 25 genomic regions. rs142667902 showed the strongest association (effect allele A; effect size ‒0.17; P = 1.7 × 10‒7), which is located near DPPA4, encoding a protein involved in pluripotency in stem cells, which are essential for repair of radiation-induced tissue injury. Gene-set enrichment analysis identified 'RNA splicing via endonucleolytic cleavage and ligation' (P = 5.1 × 10‒6, P = .079 corrected) as the top gene set associated with rSTATacute among all patients. In silico gene expression analysis showed that the genes associated with rSTATacute were statistically significantly up-regulated in skin (not sun exposed P = .004 corrected; sun exposed P = .026 corrected). CONCLUSIONS: There is shared SNV-based heritability for acute radiation-induced toxicity across and within individual cancer sites. Future meta-genome-wide association studies among large radiation therapy patient cohorts are worthwhile to identify the common causal variants for acute radiotoxicity across cancer types

Large-scale meta-genome-wide association study reveals common genetic factors linked to radiation-induced acute toxicities across cancer types.

Acknowledgements: The study sponsors were not involved in the design of the study; the collection, analysis, and interpretation of the data; the writing of the manuscript; or the decision to submit the manuscript for publication. We thank all patients who participated in the study and the participating clinic staff for their contribution to data collection. This publication presents data from the Head and Neck 5000 study. The study was a component of independent research funded by the NIHR under its Programme Grants for Applied Research scheme (RP-PG-0707-10034). The views expressed in this publication are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health. Core funding was also provided through awards from Above and Beyond, University Hospitals Bristol and Weston Research Capability Funding, and the NIHR Senior Investigator award to Professor Andy Ness. Genotyping was funded by World Cancer Research Fund Pilot Grant (grant No. 2018/1792), Above and Beyond, Wellcome Trust Research Training Fellowship (201237/Z/16/Z), and Cancer Research UK Cancer Research UK Programme Grant, the Integrative Cancer Epidemiology Programme (grant No. C18281/A19169). The VHIO authors acknowledge the Cellex Foundation for providing research equipment and facilities and thank CERCA Program/Generalitat de Catalunya for institutional support.Funder: National Institute for Health Research; DOI: https://doi.org/10.13039/501100000272Funder: The Taylor Family FoundationFunder: Cancer Research UK; DOI: https://doi.org/10.13039/501100000289Funder: National Medical Research Council; DOI: https://doi.org/10.13039/501100001349BACKGROUND: This study was designed to identify common genetic susceptibility and shared genetic variants associated with acute radiation-induced toxicity across 4 cancer types (prostate, head and neck, breast, and lung). METHODS: A genome-wide association study meta-analysis was performed using 19 cohorts totaling 12 042 patients. Acute standardized total average toxicity (STATacute) was modelled using a generalized linear regression model for additive effect of genetic variants, adjusted for demographic and clinical covariates (rSTATacute). Linkage disequilibrium score regression estimated shared single-nucleotide variation (SNV-formerly SNP)-based heritability of rSTATacute in all patients and for each cancer type. RESULTS: Shared SNV-based heritability of STATacute among all cancer types was estimated at 10% (SE = 0.02) and was higher for prostate (17%, SE = 0.07), head and neck (27%, SE = 0.09), and breast (16%, SE = 0.09) cancers. We identified 130 suggestive associated SNVs with rSTATacute (5.0 × 10‒8 < P < 1.0 × 10‒5) across 25 genomic regions. rs142667902 showed the strongest association (effect allele A; effect size ‒0.17; P = 1.7 × 10‒7), which is located near DPPA4, encoding a protein involved in pluripotency in stem cells, which are essential for repair of radiation-induced tissue injury. Gene-set enrichment analysis identified 'RNA splicing via endonucleolytic cleavage and ligation' (P = 5.1 × 10‒6, P = .079 corrected) as the top gene set associated with rSTATacute among all patients. In silico gene expression analysis showed that the genes associated with rSTATacute were statistically significantly up-regulated in skin (not sun exposed P = .004 corrected; sun exposed P = .026 corrected). CONCLUSIONS: There is shared SNV-based heritability for acute radiation-induced toxicity across and within individual cancer sites. Future meta-genome-wide association studies among large radiation therapy patient cohorts are worthwhile to identify the common causal variants for acute radiotoxicity across cancer types