A radio-detected type Ia supernova with helium-rich circumstellar material.

Type Ia supernovae (SNe Ia) are thermonuclear explosions of degenerate white dwarf stars destabilized by mass accretion from a companion star1, but the nature of their progenitors remains poorly understood. A way to discriminate between progenitor systems is through radio observations; a non-degenerate companion star is expected to lose material through winds2 or binary interaction3 before explosion, and the supernova ejecta crashing into this nearby circumstellar material should result in radio synchrotron emission. However, despite extensive efforts, no type Ia supernova (SN Ia) has ever been detected at radio wavelengths, which suggests a clean environment and a companion star that is itself a degenerate white dwarf star4,5. Here we report on the study of SN 2020eyj, a SN Ia showing helium-rich circumstellar material, as demonstrated by its spectral features, infrared emission and, for the first time in a SN Ia to our knowledge, a radio counterpart. On the basis of our modelling, we conclude that the circumstellar material probably originates from a single-degenerate binary system in which a white dwarf accretes material from a helium donor star, an often proposed formation channel for SNe Ia (refs. 6,7). We describe how comprehensive radio follow-up of SN 2020eyj-like SNe Ia can improve the constraints on their progenitor systems.

Island-specific evolution of a sex-primed autosome in a sexual planarian.

The sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite1,2. Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confirm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We find that most known master regulators5-13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome.

A very luminous jet from the disruption of a star by a massive black hole.

Tidal disruption events (TDEs) are bursts of electromagnetic energy that are released when supermassive black holes at the centres of galaxies violently disrupt a star that passes too close1. TDEs provide a window through which to study accretion onto supermassive black holes; in some rare cases, this accretion leads to launching of a relativistic jet2-9, but the necessary conditions are not fully understood. The best-studied jetted TDE so far is Swift J1644+57, which was discovered in γ-rays, but was too obscured by dust to be seen at optical wavelengths. Here we report the optical detection of AT2022cmc, a rapidly fading source at cosmological distance (redshift z = 1.19325) the unique light curve of which transitioned into a luminous plateau within days. Observations of a bright counterpart at other wavelengths, including X-ray, submillimetre and radio, supports the interpretation of AT2022cmc as a jetted TDE containing a synchrotron 'afterglow', probably launched by a supermassive black hole with spin greater than approximately 0.3. Using four years of Zwicky Transient Facility10 survey data, we calculate a rate of [Formula: see text] per gigapascals cubed per year for on-axis jetted TDEs on the basis of the luminous, fast-fading red component, thus providing a measurement complementary to the rates derived from X-ray and radio observations11. Correcting for the beaming angle effects, this rate confirms that approximately 1 per cent of TDEs have relativistic jets. Optical surveys can use AT2022cmc as a prototype to unveil a population of jetted TDEs.

Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity.

Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through variable pangenomic genes: genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, owing to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo genome assemblies of 16 diverse yeast isolates. With these assemblies, we resolved QTLs for growth on maltose, sucrose, raffinose, and oxidative stress to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also duplicate onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings show the need for highly complete genome assemblies to identify the genetic basis of trait variation.

Discovery of a rapidly evolving yeast defense factor, KTD1, against the secreted killer toxin K28.

Secreted protein toxins are widely used weapons in conflicts between organisms. Elucidating how organisms genetically adapt to defend themselves against these toxins is fundamental to understanding the coevolutionary dynamics of competing organisms. Within yeast communities, "killer" toxins are secreted to kill nearby sensitive yeast, providing a fitness advantage in competitive growth environments. Natural yeast isolates vary in their sensitivity to these toxins, but to date, no polymorphic genetic factors contributing to defense have been identified. We investigated the variation in resistance to the killer toxin K28 across diverse natural isolates of the Saccharomyces cerevisiae population. Using large-scale linkage mapping, we discovered a novel defense factor, which we named KTD1. We identified many KTD1 alleles, which provided different levels of K28 resistance. KTD1 is a member of the DUP240 gene family of unknown function, which is rapidly evolving in a region spanning its two encoded transmembrane helices. We found that this domain is critical to KTD1's protective ability. Our findings implicate KTD1 as a key polymorphic factor in the defense against K28 toxin.

Exploring the genetic architecture of protein secretion in Komagataella phaffii (Pichia pastoris) for biotechnology applications.

Improvements to the production of proteins in industrial yeast species have largely relied on generating variation in a single genetic background. A new study in PLOS Biology leverages natural genetic variation to identify genes and variants with the potential to improve protein yield.

Iguratimod, an allosteric inhibitor of macrophage migration inhibitory factor (MIF), prevents mortality and oxidative stress in a murine model of acetaminophen overdose.

BACKGROUND: Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that has been implicated in multiple inflammatory and non-inflammatory diseases, including liver injury induced by acetaminophen (APAP) overdose. Multiple small molecule inhibitors of MIF have been described, including the clinically available anti-rheumatic drug T-614 (iguratimod); however, this drug's mode of inhibition has not been fully investigated. METHODS: We conducted in vitro testing including kinetic analysis and protein crystallography to elucidate the interactions between MIF and T-614. We also performed in vivo experiments testing the efficacy of T-614 in a murine model of acetaminophen toxicity. We analyzed survival in lethal APAP overdose with and without T-614 and using two different dosing schedules of T-614. We also examined MIF and MIF inhibition effects on hepatic hydrogen peroxide (H2O2) as a surrogate of oxidative stress in non-lethal APAP overdose. RESULTS: Kinetic analysis was consistent with a non-competitive type of inhibition and an inhibition constant (Ki) value of 16 µM. Crystallographic analysis revealed that T-614 binds outside of the tautomerase active site of the MIF trimer, with only the mesyl group of the molecule entering the active site pocket. T-614 improved survival in lethal APAP overdose when given prophylactically, but this protection was not observed when the drug was administered late (6 h after APAP). T-614 also decreased hepatic hydrogen peroxide concentrations during non-lethal APAP overdose in a MIF-dependent fashion. CONCLUSIONS: T-614 is an allosteric inhibitor of MIF that prevented death and decreased hepatic hydrogen peroxide concentrations when given prophylactically in a murine model of acetaminophen overdose. Further studies are needed to elucidate the mechanistic role of MIF in APAP toxicity.

The Benefit of Cost-Transparency Calculators Does Not Extend to Vascular Surgery Patients.

BACKGROUND: In 2021, the Centers for Medicare & Medicaid Services (CMS) mandated that every hospital create a publicly available webtool for pricing various medical services in an effort to give patients transparency in regard to their health care expenses and allow patients to "shop around" to receive the care most fitting their budget. Our objective is to investigate the utility this mandate provides for vascular surgery patients. METHODS: Standardized searches were performed to find patient cost calculators for Newsweek's Top 50 Hospitals in the United States. If the webtool was found, a list of standardized searches were performed to investigate whether the tool listed prices for the following vascular procedures: Arteriovenous fistula (AVF), varicose vein procedures, and Endovascular Aneurysm Repair (EVAR). RESULTS: Of the 50 hospitals included, all had an easily accessible web-based cost estimator tool. The average time to find the cost estimator was 33.27 sec. Of these 50 hospitals, 10% provided cost information on AVF surgery, 12% provided cost information on varicose vein procedures, and 0% provided information on EVAR. There was no difference in the hospital's likelihood to report a price based on region of the United States. Average preinsurance price for AVF surgery was $11,933.61 and $22,191 for vein procedures. CONCLUSIONS: In conclusion, despite good adherence to the CMS mandate requiring a publicly available pricing tool, these tools provide little to no information for vascular surgery patients. Overall, this discrepancy places vascular surgery patients at a significant disadvantage. As such, vascular patients do not have access to the knowledge necessary to financially prepare for surgery, and furthermore, they are not afforded the luxury to choose where to have procedures performed based on price variability. Hopefully this research will encourage hospitals to broaden the scope of their cost calculators to allow it to benefit all patients.

Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos.

The squamates (lizards and snakes) are close relatives of birds and mammals, with more than 10,000 described species that display extensive variation in a number of important biological traits, including coloration, venom production, and regeneration. Due to a lack of genomic tools, few genetic studies in squamates have been carried out. The leopard gecko, Eublepharis macularius, is a popular companion animal, and displays a variety of coloration patterns. We took advantage of a large breeding colony and used linkage analysis, synteny, and homozygosity mapping to investigate a spontaneous semi-dominant mutation, "Lemon Frost", that produces white coloration and causes skin tumors (iridophoroma). We localized the mutation to a single locus which contains a strong candidate gene, SPINT1, a tumor suppressor implicated in human skin cutaneous melanoma (SKCM) and over-proliferation of epithelial cells in mice and zebrafish. Our work establishes the leopard gecko as a tractable genetic system and suggests that a tumor suppressor in melanocytes in humans can also suppress tumor development in iridophores in lizards.

Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells.

Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci, and three loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene. Divergent properties were displayed by the RH-BSA growth genes compared to those from loss-of-function screens, refuting the balance hypothesis. In addition, enhanced retention of human centromeres in the RH pools suggests a new approach to functional dissection of these chromosomal elements. Pooled analysis of RH cells showed high power and resolution and should be a useful addition to the mammalian genetic toolkit.

Post-Mastectomy Tissue Expander Placement Followed by Radiation Therapy: A Cost-Effectiveness Analysis of Staged Autologous Versus Implant-Based Unilateral Reconstruction.

BACKGROUND: There is no preferred approach to breast reconstruction for patients with locally advanced breast cancer (LABC) who require post-mastectomy radiation therapy (PMRT). Staged implant and autologous reconstruction both have unique risks and benefits. No previous study has compared their cost-effectiveness with utility scores. METHODS: A literature review determined the probabilities and outcomes for mastectomy and staged implant or autologous reconstruction. Utility scores were used to calculate the quality-adjusted life years (QALYs) associated with successful surgery and postoperative complications. Medicare billing codes were used to assess costs. A decision analysis tree was constructed with rollback and incremental cost-effectiveness ratio (ICER) analyses. Sensitivity analyses were performed to validate results and account for uncertainty. RESULTS: Mastectomy with staged deep inferior epigastric perforator (DIEP) flap reconstruction is costlier ($14,104.80 vs $3216.93), but more effective (QALYs, 29.96 vs 24.87). This resulted in an ICER of 2141.00, favoring autologous reconstruction. One-way sensitivity analysis showed that autologous reconstruction was more cost-effective if less than $257,444.13. Monte Carlo analysis showed a confidence of 99.99% that DIEP flap reconstruction is more cost-effective. CONCLUSIONS: For patients with LABC who require PMRT, staged autologous reconstruction is significantly more cost-effective than reconstruction with implants. Despite the decreased morbidity, staged implant reconstruction has greater rates of complication.

Variable Accessibility to Consumer Pricing Among Breast Cancer Operations.

BACKGROUND: The Centers for Medicare & Medicaid Services (CMS) mandate that every US hospital provide public online pricing information for services rendered. This allows patients to compare prices across hospital systems before establishing care. The goal of this project was to evaluate hospital compliance and patient-level accessibility to price transparency for common breast cancer surgical procedures. METHODS: A sample case of a 62-year-old female with a T2N0 breast cancer was chosen. The patient would have the option of undergoing a partial mastectomy or mastectomy, both with sentinel lymph node biopsy (SLNB). Eight Massachusetts academic medical centers were evaluated. Searches were performed by authors for each hospital system and procedure using the sample case. RESULTS: Every hospital had a cost calculator on its website. The average success rate of establishing a cost for partial mastectomy, mastectomy, and SLNB was 58, 35, and 25%, respectively. The median time to reach the cost calculator tool was 32 s (range 25-37 s). In successful attempts, the median pre-insurance estimated cost of a partial mastectomy was $16,509 (range $11,776-22,169), compared with $24,541 (range $16,921-25,543) for mastectomy and $12,342 (range $4034-20,644) for SLNB. SLNB costs varied significantly across hospitals (p = 0.025), but no statistically significant difference was observed for partial mastectomy or mastectomy. CONCLUSION: Despite new regulatory requirements by CMS for increased price transparency for surgical procedures, our results demonstrate poor success rates in obtaining cost estimates and significant variability of reported hospital charges. Further efforts to improve the quality of hospital cost estimate calculators are necessary for informed decision-making for patients with breast cancer.

Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for "polygenic epistasis".

BACKGROUND: The majority of quantitative genetic models used to map complex traits assume that alleles have similar effects across all individuals. Significant evidence suggests, however, that epistatic interactions modulate the impact of many alleles. Nevertheless, identifying epistatic interactions remains computationally and statistically challenging. In this work, we address some of these challenges by developing a statistical test for polygenic epistasis that determines whether the effect of an allele is altered by the global genetic ancestry proportion from distinct progenitors. RESULTS: We applied our method to data from mice and yeast. For the mice, we observed 49 significant genotype-by-ancestry interaction associations across 14 phenotypes as well as over 1,400 Bonferroni-corrected genotype-by-ancestry interaction associations for mouse gene expression data. For the yeast, we observed 92 significant genotype-by-ancestry interactions across 38 phenotypes. Given this evidence of epistasis, we test for and observe evidence of rapid selection pressure on ancestry specific polymorphisms within one of the cohorts, consistent with epistatic selection. CONCLUSIONS: Unlike our prior work in human populations, we observe widespread evidence of ancestry-modified SNP effects, perhaps reflecting the greater divergence present in crosses using mice and yeast.

Retrospective Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Symptomatic Patients Prior to Widespread Diagnostic Testing in Southern California.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused one of the worst pandemics in recent history. Few reports have revealed that SARS-CoV-2 was spreading in the United States as early as the end of January. In this study, we aimed to determine if SARS-CoV-2 had been circulating in the Los Angeles (LA) area at a time when access to diagnostic testing for coronavirus disease 2019 (COVID-19) was severely limited. METHODS: We used a pooling strategy to look for SARS-CoV-2 in remnant respiratory samples submitted for regular respiratory pathogen testing from symptomatic patients from November 2019 to early March 2020. We then performed sequencing on the positive samples. RESULTS: We detected SARS-CoV-2 in 7 specimens from 6 patients, dating back to mid-January. The earliest positive patient, with a sample collected on January 13, 2020 had no relevant travel history but did have a sibling with similar symptoms. Sequencing of these SARS-CoV-2 genomes revealed that the virus was introduced into the LA area from both domestic and international sources as early as January. CONCLUSIONS: We present strong evidence of community spread of SARS-CoV-2 in the LA area well before widespread diagnostic testing was being performed in early 2020. These genomic data demonstrate that SARS-CoV-2 was being introduced into Los Angeles County from both international and domestic sources in January 2020.

Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks. METHODS: The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020. RESULTS: We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region. CONCLUSION: Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic.

Analysis of the genetic basis of height in large Jewish nuclear families.

Despite intensive study, most of the specific genetic factors that contribute to variation in human height remain undiscovered. We conducted a family-based linkage study of height in a unique cohort of very large nuclear families from a founder (Jewish) population. This design allowed for increased power to detect linkage, compared to previous family-based studies. Loci we identified in discovery families could explain an estimated lower bound of 6% of the variance in height in validation families. We showed that these loci are not tagging known common variants associated with height. Rather, we suggest that the observed signals arise from variants with large effects that are rare globally but elevated in frequency in the Jewish population.

A Cost-Utility Analysis Comparing Immediate Oncoplastic Surgery with Delayed Oncoplastic Surgery in Smoking Breast Cancer Patients.

BACKGROUND: Oncoplastic reduction mammoplasty for smoking breast cancer patients committed to smoking cessation may be performed immediately (increasing smoking-related risk) or in a delayed fashion (increasing radiation-related risk). OBJECTIVE: Our aim was to examine the cost utility of immediate versus delayed oncoplastic reconstruction when operating on a smoking patient with breast cancer and macromastia with a long-term commitment to smoking cessation. METHODS: A literature review determined the probabilities and outcomes for the treatment of unilateral breast cancer with immediate or delayed oncoplastic surgery. Reported utility scores were used to estimate quality-adjusted life-years (QALYs) for varying health states. A decision analysis tree was constructed with rollback analysis to highlight the more cost-effective strategy, and an incremental cost-utility ratio (ICUR) was calculated. Sensitivity analyses were performed to validate the robustness of the results. RESULTS: Immediate oncoplastic surgery is associated with a higher clinical effectiveness (QALY) of 33.3 compared with delayed oncoplastic surgery (33.26), with a higher increment of clinical effectiveness of 0.07 and relative cost reduction of $3458.11. This resulted in a negative ICUR of -50,194, which favored immediate reconstruction, indicating a dominant strategy. In one-way sensitivity analyses, delayed reconstruction was the more cost-effective strategy if the probability of successful immediate reconstruction falls below 29% or its cost exceeds $29,611. Monte-Carlo analysis showed a confidence of 99% that immediate oncoplastic surgery is more cost effective. CONCLUSIONS: Despite the risk of postoperative complications associated with smoking, immediate oncoplastic surgery is more cost effective compared with delayed oncoplastic surgery in which reconstructive surgery would occur after radiation.

Discordance in Oncotype DX Breast Recurrence Score® Results for Bilateral Breast Cancer.

BACKGROUND: The Oncotype DX Breast Recurrence Score® assay is a clinically useful tool to determine the benefit of chemotherapy in the treatment of early-stage, hormone-receptor-positive breast cancer. Bilateral breast cancer (BBC) is found in ~ 5% of patients with breast cancer, and data regarding discordance of Oncotype DX results between BBC defined by current TAILORx subgroups are limited. Our goals are to study the rate of Oncotype DX discordance between BBC and investigate whether such differences can affect chemotherapy treatment discussions. METHODS: Patients with BBC were identified in US samples submitted to Genomic Health for 21-gene testing between January 2019 and July 2020. The risk categories were defined as 0-25 and 26-100 as well as 0-17, 18-30, and 31-100 for all patients. Subgroup analysis was also performed for node-negative women age ≤ 50 years with Recurrence Score results of 0-15, 16-20, 21-25, and 26-100. RESULTS: 944 BBC patients with known nodal status (702 node negative, 242 node positive) were identified and included. Among node-negative patients aged > 50 years, the rate of discordance in Recurrence Score by group (0-25 and 26-100) was 4.2% (n = 598). For node-negative patients aged ≤ 50 years, the risk group was discordant in < 3% when considering the risk grouping of 0-25 and 26-100. However, upon subgroup analysis based on TAILORx analysis, the rate of discordance was 48.1% in these younger patients (n = 104). CONCLUSIONS: This study shows that a clinically relevant rate of discordance in Oncotype DX results in patients with BBC may impact medical decision-making regarding chemotherapy.