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Julie Beyrer,1,&ast; David R Nelson,1,&ast; Kristin M Sheffield,1,&ast; Yu-Jing Huang,1,&ast; Yiu-Keung Lau,1,&ast; Ana L Hincapie2,&ast; 1Eli Lilly and Company, Indianapolis, IN, USA; 2University of Cincinnati James L. Winkle College of Pharmacy, Cincinnati, OH, USA&ast;These authors contributed equally to this workCorrespondence: Julie Beyrer, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA, Tel +1 317 651 8236, Email beyrerj@lilly.comPurpose: We sought to develop and validate an incident non-small cell lung cancer (NSCLC) algorithm for United States (US) healthcare claims data. Diagnoses and procedures, but not medications, were incorporated to support longer-term relevance and reliability.Methods: Patients with newly diagnosed NSCLC per Surveillance, Epidemiology, and End Results (SEER) served as cases. Controls included newly diagnosed small-cell lung cancer and other lung cancers, and two 5% random samples for other cancer and without cancer. Algorithms derived from logistic regression and machine learning methods used the entire sample (Approach A) or started with a previous algorithm for those with lung cancer (Approach B). Sensitivity, specificity, positive predictive values (PPV), negative predictive values, and F-scores (compared for 1000 bootstrap samples) were calculated. Misclassification was evaluated by calculating the odds of selection by the algorithm among true positives and true negatives.Results: The best performing algorithm utilized neural networks (Approach B). A 10-variable point-score algorithm was derived from logistic regression (Approach B); sensitivity was 77.69% and PPV = 67.61% (F-score = 72.30%). This algorithm was less sensitive for patients ≥ 80 years old, with Medicare follow-up time < 3 months, or missing SEER data on stage, laterality, or site and less specific for patients with SEER primary site of main bronchus, SEER summary stage 2000 regional by direct extension only, or pre-index chronic pulmonary disease.Conclusion: Our study developed and validated a practical, 10-variable, point-based algorithm for identifying incident NSCLC cases in a US claims database based on a previously validated incident lung cancer algorithm.Keywords: algorithm, machine learning, medicare claims, non-small cell lung cancer, positive predictive value, sensitivity, validation

Diterpenoid biosynthesis in plants is derived from photosynthetic pigment metabolism, and arose early in land plant evolution, enabling stockpiling of the extensive arsenal of (di)terpenoid natural products currently observed in this kingdom.

To develop a claims-based algorithm identifying systemic lupus erythematosus (SLE) flares using a linked claims-electronic medical record (EMR) dataset. This study was a retrospective analysis of linked administrative claims and EMR data spanning 1 January 2003 to 31 March 2019. Included were adult SLE patients with at least 12 months of continuous enrollment in claims data, 12 months of clinical activity in EMR, and an absence of malignancies excluding basal and squamous cell carcinoma. Patient follow-up was divided into 30-day windows, and a proxy SLEDAI-2K score based on the EMR data was calculated for each 30-day period. A flare was defined as an increase of at least 4 from the baseline score. A series of potential flare predictor variables identified in claims were based on a combination of established variables from a previous algorithm, with the addition of other SLE-related indicators based on clinical input. Logistic regression models were built to predict monthly SLE flares. Inclusion criteria identified 2427 patients. Results from a logistic model with forward selection capping the number of variables at 10 performed well with a c-statistic of 0.76 and a Brier score of 0.07. The top five predictors were any inpatient admission (OR = 4.76), outpatient office visit (OR = 3.04), MRI (OR = 2.26), ER visit (OR = 2.25), and number of rheumatology visits (OR = 1.75); p < .01 for all. The final algorithm shows promise in providing an alternative and more streamlined way for identifying likely flares in administrative claims data that will advance the study of SLE within the context of flares.

Background. Despite high efficacy rates for direct acting antiviral regimens to cure hepatitis C virus infection, many patients experience treatment-related symptoms. Accurate reporting of adverse events is mandatory to determine drug safety. Previous research in other medical conditions has documented discordance between clinician-reported and patient-reported symptomatic adverse events. Aims. To explore concordance and associated factors, between clinician-recorded and patient-reported fatigue, headache, and nausea/vomiting during a clinical trial of three treatment regimens. Methods. Data were collected between treatment start and 31 days posttreatment. Patients completed Patient-Reported Outcomes Measurement Information System measures of fatigue and nausea/vomiting and the Headache Impact Test. Clinician-recorded data were abstracted from medical records. Concordance was evaluated by weighted kappa. Demographic and clinical factors associated with concordance were identified using logistic regression models. Results. Participants included 1,058 patients treated for chronic hepatitis C (average 54.9 years; 43% Black; 59% male). Weighted kappa estimates and 95% confidence intervals between patients (no/mild vs. moderate/severe symptoms) and clinicians (not present vs. present) were fatigue ( k = 0.09 , 0.02-0.16), headache ( k = 0.08 , 0.02-0.14), and nausea/vomiting ( k = 0.20 , 0.11-0.28). Older age and having private insurance (compared to Medicaid) were associated with better headache concordance. Older age, male, absence of psychiatric condition, and ≤2 comorbidities were associated with better nausea/vomiting concordance. Conclusions. Poor concordance was observed between patient-reported and clinician-recorded symptomatic adverse events. Despite study limitations, previous literature in other conditions support these findings. Integrating patient-reported data to inform adverse event reporting would improve evaluations of treatment safety (http://CT.gov/ Registration: NCT02786537).

The PRIORITIZE trial (clinicaltrials.gov: NCT02786537) was the first comparative effectiveness study to directly compare ledipasvir/sofosbuvir (LDV/SOF) and elbasvir/grazoprevir (EBR/GZR) for the treatment of chronic hepatitis C virus (HCV). A secondary aim of this study was to compare LDV/SOF and EBR/GZR on sustainable changes in several HCV-associated symptoms and functional well-being in patients who achieved sustained virological response (SVR). PRIORITIZE, a randomized controlled trial conducted between 2016 and 2020, evaluated change in six PROMIS® symptom scores (fatigue, sleep disturbance, cognitive disturbance, nausea, diarrhoea, abdominal pain) and functional well-being using the disease-specific HCV-PRO instrument. Survey assessments were administered at baseline, early post-treatment (median = 6 months) and late post-treatment (median = 21 months). Constrained longitudinal linear mixed-effects models were used to evaluate within-treatment change and between-treatment differences. Data from 793 participants (average 55 years old, 57% male, 44% black, 17% with cirrhosis) were analysed. From baseline to early post-treatment, 5 out of 6 symptoms and functional well-being significantly improved (all p's .05). In the LDV/SOF arm, mean changes ranged from -3.73 for nausea to -6.41 for fatigue and in the EBR/GZR, mean changes ranged from -2.19 for cognitive impairment to -4.67 for fatigue. Change of3 points was consider clinically meaningful. Improvements in most symptoms slightly favoured LDV/SOF, although the magnitude of differences between the regimens were small. Both regimens demonstrated significant improvements in symptoms and functional well-being that were sustained during the late post-treatment phase. EBR/GZR and LDV/SOF regimens had clinically equivalent and durable improvements in HCV symptoms and functional well-being up to two years after SVR.

Here, we announce the draft genome sequence of Vibrio parahaemolyticus strain PSU5579, isolated from a shrimp hatchery in southern Thailand during an outbreak of acute hepatopancreatic necrosis disease (AHPND). The genome contains 44 contigs with a sequence length of 5,229,426 bp, 4,861 coding sequences, and a G+C content of 45.3%.

Background & Aims Retreatment with glecaprevir/pibrentasvir (G/P) resulted in a rate of sustained virologic response 12 weeks after treatment completion (SVR12) of >90% in HCV genotype 1 (GT1) patients who previously failed a regimen of sofosbuvir plus an NS5A inhibitor (NS5Ai). This study investigated the prevalence and impact of baseline NS3 and NS5A resistance-associated substitutions (RASs) on the efficacy of G/P in prior GT1 sofosbuvir+NS5Ai failures and the persistence of treatment-emergent RASs. Methods Longitudinal samples from 177 patients enrolled in a phase IIIb, randomized pragmatic clinical trial were analyzed. Patients without cirrhosis were randomized to 12 or 16 weeks of G/P, and patients with compensated cirrhosis were randomized to G/P and ribavirin for 12 weeks or G/P for 16 weeks. Linkage of RAS was identified using Primer-ID next-generation sequencing at a 15% cut-off. Results Of 177 patients, 169 (95.5%) were PI-naive. All 33 GT1b-infected patients achieved SVR12. In GT1a-infected patients, baseline NS5A RASs were prevalent (74.5%, 105/141) but NS3 RASs were uncommon. Baseline NS3 RASs had no impact on G/P efficacy and patients with baseline NS5A RASs showed a numerically but not statistically significantly lower SVR12 rate compared to those without NS5A RASs (89% vs. 97%). SVR12 was achieved in 34 of 35 (97%) patients without NS5A baseline substitution, and 53 of 57 (93%), 35 of 40 (88%), 5 of 8 (63%) with single, double-linked, and triple-linked NS5A substitutions, respectively. Among 13 patients with virologic failure, 4 acquired treatment-emergent NS3 RASs and 10 acquired NS5A RASs. Conclusion Baseline NS5A RASs were highly prevalent. The presence of an increasing number of linked NS5A RASs in GT1a showed a trend in decreasing SVR12 rates, although no specific NS5A RASs or their linkage pattern were associated with lower SVR12 rates. Lay summary Direct-acting antivirals have revolutionized the treatment of chronic hepatitis C infection, but treatment failure occurs in some patients. Retreatment of patients who previously failed a regimen consisting of sofosbuvir and an NS5A inhibitor with a regimen of glecaprevir and pibrentasvir (G/P) is >90% effective. Herein, we analyzed samples from these patients and showed that retreatment efficacy with G/P is lower in patients with double- or triple-linked NS5A resistance mutations than in patients with single or no NS5A resistance mutations. Clinical trial number NCT03092375 .

Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the domains of life have been confined to observing the abundance of Fe-S cluster types (2Fe-2S, 3Fe-4S, 4Fe-4S, 7Fe-8S (3Fe-4s and 4Fe-4S) and 2[4Fe-4S]) and the diversity of ferredoxins within these cluster types was not studied. To address this research gap, here we propose a subtype classification and nomenclature for ferredoxins based on the characteristic spacing between the cysteine amino acids of the Fe-S binding motif as a subtype signature to assess the diversity of ferredoxins across the living organisms. To test this hypothesis, comparative analysis of ferredoxins between bacterial groups, Alphaproteobacteria and Firmicutes and ferredoxins collected from species of different domains of life that are reported in the literature has been carried out. Ferredoxins were found to be highly diverse within their types. Large numbers of alphaproteobacterial species ferredoxin subtypes were found in Firmicutes species and the same ferredoxin subtypes across the species of Bacteria, Archaea, and Eukarya, suggesting shared common ancestral origin of ferredoxins between Archaea and Bacteria and lateral gene transfer of ferredoxins from prokaryotes (Archaea/Bacteria) to eukaryotes. This study opened new vistas for further analysis of diversity of ferredoxins in living organisms.

Hepatic encephalopathy (HE) is a complex and reversible neuropsychiatric syndrome that is associated with growing, substantial healthcare resource utilization. We aim to examine the predictors of 30-day readmission and hospitalization cost associated with HE. We conducted a cross-sectional study using the Nationwide Readmissions Database from 2010 to 2014. We assessed the readmission rates using multivariate logistic regression and established temporal trends of readmission rates and hospitalization cost. Weighted hierarchical logistic regression and generalized linear mixed models were used to identify predictors for nationally representative readmissions and hospitalization costs, respectively. The number of index hospitalizations with HE increased with a significant trend from 34,967 in 2010 to 44,791 in 2014. 16.8% of patients were readmitted within 30 days. Predictors increasing readmission risk included female sex, Elixhauser readmission score < 25, elective admission, patient’s state residential status, privately insured, number of diagnoses >13, and length of stay >4 days. Our results indicate there is a need to implement better management strategies to improve outcomes in patients hospitalized with HE to curb the increase in the economic burden associated with the disease.

BACKGROUND AND AIMS Our aim was to evaluate the impact of direct-acting antivirals (DAAs) on decompensated cirrhosis (DCC) and HCC in patients with chronic HCV and substance use disorder (SUD) compared with those without an SUD. APPROACH AND RESULTS This retrospective cohort study used the MarketScan database (2013-2018) to identify 29,228 patients with chronic HCV, where 22% (n = 6,385) had ≥1 SUD diagnosis. The inverse probability of treatment weighted multivariable Cox proportional hazard models were used to compare the risk of developing DCC and HCC. Among the those who were noncirrhotic, treatment reduced the DCC risk among SUD (adjusted hazard ratio [aHR] 0.13; 95% CI, 0.06-0.30) and non-SUD (aHR 0.11; 95% CI, 0.07-0.18), whereas the risk for HCC was not reduced for the SUD group (aHR 0.91; 95% CI, 0.33-2.48). For those with cirrhosis, compared with patients who were untreated, treatment reduced the HCC risk among SUD (aHR, 0.33; 95% CI, 0.13-0.88) and non-SUD (aHR, 0.40; 95% CI, 0.25-0.65), whereas the risk for DCC was not reduced for the SUD group (aHR, 0.64; 95% CI, 0.37-1.13). Among patients with cirrhosis who were untreated, the SUD group had a higher risk of DCC (aHR, 1.52; 95% CI, 1.03-2.24) and HCC (aHR, 1.69; 95% CI, 1.05-2.72) compared with non-SUD group. CONCLUSIONS Among the HCV SUD group, DAA treatment reduced the risk of DCC but not HCC for those who were noncirrhotic, whereas DAA treatment reduced the risk of HCC but not DCC for those with cirrhosis. Among the nontreated, patients with an SUD had a significantly higher risk of DCC and HCC compared with those without an SUD. Thus, DAA treatment should be considered for all patients with HCV and an SUD while also addressing the SUD.

INTRODUCTION: Pangenotypic, all-oral direct-acting antivirals, such as glecaprevir/pibrentasvir (G/P), are recommended for treatment of hepatitis C virus (HCV) infection. Concerns exist about the impact on efficacy in patients with suboptimal adherence, particularly with shorter treatment durations. These post hoc analyses evaluated adherence (based on pill count) in patients prescribed 8- or 12-week G/P, the impact of nonadherence on sustained virologic response at post-treatment week 12 (SVR12), factors associated with nonadherence, and efficacy in patients interrupting G/P treatment. METHODS: Data were pooled from 10 phase 3 clinical trials of treatment-naive patients with HCV genotype 1–6 without cirrhosis/with compensated cirrhosis (treatment adherence analysis) and 13 phase 3 clinical trials of all patients with HCV (interruption analysis). RESULTS: Among 2,149 patients included, overall mean adherence was 99.4%. Over the treatment duration, adherence decreased (weeks 0–4: 100%; weeks 5–8: 98.3%; and weeks 9–12: 97.1%) and the percentage of patients with ≥80% or ≥90% adherence declined. SVR12 rate in the intention-to-treat (ITT) population was 97.7% (modified ITT SVR12 99.3%) and remained high in nonadherent patients in the modified ITT population (

In the United States, Black people are disproportionately diagnosed with hepatitis C virus (HCV) compared with White people but are under-represented in HCV studies. In this US-based cross-sectional telephone survey study, we assessed willingness to participate (WTP) in health/medical research and attitudes and beliefs that may influence WTP among Black patients with HCV. Two hundred participants who had current or prior HCV diagnosis and self-identified as Black or African American were recruited from a national HCV cohort study and an outpatient hepatology clinic. WTP responses ranged from 1 (not at all willing) to 5 (very willing). Multivariable models were used to identify factors associated with the overall mean WTP score. In addition, an open-ended question solicited strategies to help increase research participation from the Black community. Overall, participants reported moderate WTP in research (Mean [95% Confidence Interval (CI)] = 3.78 [3.68, 3.88]). Of 13 types of research presented, participants reported lowest WTP for randomized controlled trials of medications (Mean [95% CI] = 2.31 [2.11, 2.50]). The initial multivariable model identified higher subjective knowledge of research as positively associated with WTP (Parameter estimate [95% CI] = 0.15 [0.02, 0.27]). Sensitivity analyses also identified higher perceived benefits of research as an additional factor associated with WTP. Qualitative findings indicate that greater community-based outreach efforts would increase accessibility of research opportunities. When given the opportunity to participate, Black participants with HCV reported moderate WTP in health/medical research. Research sponsors and investigators should employ community-based outreach to expand access and awareness of research opportunities.

The ADA recommends that all people with diabetes at risk of level 2 or 3 hypoglycemia be prescribed glucagon. Studies of conventional reconstituted injectable glucagon showed low rates of successful delivery of a full dose and low prescription filling rates. Since July 2019, ready-to-use glucagon options have become commercially available. IBM® MarketScan® Research Database was used to study prescription patterns among people with T1D or T2D on insulin who had filled a glucagon prescription 2 years prior to July 2019 (pre-period) and/or 2 years after through July 2021 (post-period) . Logistic regression models (for feature selection of independent variables followed by two-way interaction identification from Multivariate Adaptive Regression Splines) were utilized to determine glucagon fills post-period based on variables pre-period (demographics, diabetes type, insurance, comorbidities, history of hypoglycemia, diabetes medications) . Classification trees were used to illustrate the effects of significant variables (variables added >1% accuracy from cross validation) . Of all insulin-treated people (n=138,826) over the 4-year period, 13.5% (T1D 48.4%, T2D 3.5%) had glucagon prescriptions filled. Of those who filled glucagon post-period (n=14,234) , 54.3% filled a ready-to-use glucagon. The primary drivers and % of glucagon fills post-period: overall included age Disclosure B. Mitchell: Employee; Eli Lilly and Company, Stock/Shareholder; Eli Lilly and Company. D. R. Nelson: Employee; Eli Lilly and Company. A. Meeks: Employee; Eli Lilly and Company. Y. Yan: Employee; Eli Lilly and Company. Funding Eli Lilly and Company

Background: HbA1c is a primary measure of glycemic control and managing HbA1c may help reduce the risk of complications. This study aimed to describe trends in HbA1c by insulin regimen. Methods: This was a retrospective analysis of cross-sectional surveys collected from the National Health and Nutrition Examination Survey between 2009-2018. Mean HbA1c and proportion achieving guideline- and HCP-recommended (i.e. personalized) HbA1c targets were evaluated in aggregate and over time in adults (18-64 years) with type 1 (T1DM) or type 2 (T2DM) diabetes using mealtime insulin (MTI) or basal insulin only. Trends over time between 2009-2018 were evaluated after adjusting for age, gender, race/ethnicity. The analysis included the strata, clusters, and weighting of the complex survey design. Results: From 2009-2018, 26.1% of people with T1DM (weighted n=891,194; mean HbA1c [SE] 7.9% [0.2]) , 24.8% with T2DM MTI (weighted n=1,591,183; mean HbA1c [SE] 8.6% [0.2]) , and 11.2% with T2DM basal only (weighted n=1,087,895; mean HbA1c [SE] 8.6% [0.2]) achieved the ADA recommended HbA1c goal of Conclusions: Across all insulin regimens based off the most recent NHANES data, ∼75-90% of individuals are not achieving ADA-recommended or personalized HbA1c goals. Emerging treatment tools (e.g. new technologies, advanced insulins, and time in range metrics) may facilitate improved diabetes outcomes. Disclosure E.R.Hankosky: Employee; Eli Lilly and Company, Stock/Shareholder; Eli Lilly and Company. D.Schapiro: Employee; Eli Lilly and Company. K.B.Gunn: Employee; Eli Lilly and Company. E.Lubelczyk: Employee; Eli Lilly and Company. J.Mitroi: None. D.R.Nelson: Employee; Eli Lilly and Company. Funding Eli Lilly and Company

Conical surfaces, with a δ function of Gaussian curvature at the apex, are perhaps the simplest example of geometric frustration. We study two-dimensional liquid crystals with p-fold rotational symmetry (p-atics) on the surfaces of cones. For free boundary conditions at the base, we find both the ground state(s) and a discrete ladder of metastable states as a function of both the cone angle and the liquid crystal symmetry p. We find that these states are characterized by a set of fractional defect charges at the apex and that the ground states are in general frustrated due to effects of parallel transport along the azimuthal direction of the cone. We check our predictions for the ground-state energies numerically for a set of commensurate cone angles (corresponding to a set of commensurate Gaussian curvatures concentrated at the cone apex), whose surfaces can be polygonized as a perfect triangular or square mesh, and find excellent agreement with our theoretical predictions.

Background and aims The long-term impact of hepatitis C virus (HCV) therapy with all-oral direct-acting antivirals (DAAs) on patient-reported outcomes (PROs) has not been well-described. We characterized changes in PROs from pre-treatment to 12 months post-treatment in a real-world cohort. Methods PROP UP was a multi-center observational cohort study of 1,601 patients treated with DAAs at 11 U.S. gastroenterology/hepatology practices from 2015-2017. PROs were evaluated pre-treatment (T1) and 12 months post-treatment (T5). A minimally important change (MIC) threshold was prespecified as >5% change in PRO scores from T1 to T5. Multivariable analyses identified predictors of change. Results Three-quarters of patients were 55 or older; 45% were female, 60% were white, 33% were black, nearly half had cirrhosis. The most commonly-prescribed DAA regimens were sofosbuvir-based (83%) and grazoprevir/elbasvir (11%). Study retention was greater than 95%. On average, small improvements were observed at 3 months post-treatment in all PROs and sustained at 12 months post-treatment among patients with sustained virologic response (SVR). Clinically meaningful improvements were achieved in fatigue (mean change score: -3.7 [-4.2, -3.1]), sleep (mean change score: -3.1 [-3.7, -2.5]), abdominal pain (mean change score: -2.6 [-3.3, -1.9]) and functional well-being (mean change score: -7.0 [-6.0, -8.0]). Symptom improvements were generally not sustained with no SVR (n=52). Patients with cirrhosis and MELD ≥ 12 had the greatest improvements in functional well-being (-12.9 [-17.6, -8.1]). Conclusions The improvements in patient-reported outcomes reported by patients who achieved SVR following HCV DAA therapy were durable at 12 months post-treatment.

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4–10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4–1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

Chrysodeixis includens (Walker, [1858]) is one of the most important defoliator of soybean in Brazil because of its extensive geographical distribution and high tolerance to insecticides compared with other species of caterpillars. Because of this, we conducted bioassays to evaluate the efficacy of pyrethroid λ-cyhalothrin on a C. includens resistant strain (MS) and a susceptible (LAB) laboratory strain. High throughput RNA sequencing (RNA-seq) of larval head and body tissues were performed to identify potential molecular mechanisms underlying pyrethroid resistance. Insecticide bioassays showed that MS larvae exhibit 28.9-fold resistance to pyrethroid λ-cyhalothrin relative to LAB larvae. RNA-seq identified evidence of metabolic resistance in the head and body tissues: 15 cytochrome P450 transcripts of Cyp6, Cyp9, Cyp4, Cyp304, Cyp307, Cyp337, Cyp321 families, 7 glutathione-S-transferase (Gst) genes, 7 α-esterase genes from intracellular and secreted catalytic classes, and 8 UDP-glucuronosyltransferase (Ugt) were overexpressed in MS as compared with LAB larvae. We also identified overexpression of GPCR genes (CiGPCR64-like and CiGPCRMth2) in the head tissue. To validate RNA-seq results, we performed RT-qPCR to assay selected metabolic genes and confirmed their expression profiles. Specifically, CiCYP9a101v1, CiCYP6ae149, CiCYP6ae106v2, CiGSTe13, CiCOE47, and CiUGT33F21 exhibited significant overexpression in resistant MS larvae. In summary, our findings detailed potential mechanisms of metabolic detoxification underlying pyrethroid resistance in C. includens.

We present 40Ar/39Ar ages and boron isotopes of tourmalines from a quartz-tourmaline intrusion cross-cutting the Hadean detrital-zircon-bearing metasedimentary rocks from the Mt. Alfred and Brooking Hills localities of the Illaara Greenstone Belt, Western Australia. Concordant 40Ar/39Ar plateau ages on the tourmalines at Mt. Alfred give a weighted mean age of 2935 ± 9 Ma (2σ). These results are the first reported Archean 40Ar/39Ar ages directly obtained on tourmaline, and provide a minimum depositional age for this sequence, placing constraints on the depositional timing of detrital Hadean zircons to between 2935 ± 9 Ma and c.a. 3250 Ma (youngest detrital zircon age in sequence). This is the last known occurrence of abundant detrital Hadean zircons having been directly deposited in a sedimentary sequence, and thus suggests that most Hadean zircon sources have been exhausted by this time. The 2935 ± 9 Ma tourmalines occur within a quartz-tourmaline intrusion with associated stratiform layers and veins, inferred to have grown during a hydrothermal fluid circulation event. A younger generation of tourmalines from the Brooking Hills, 30 km south of Mt. Alfred yielded concordant 40Ar/39Ar plateau ages with a weighted mean age of 2624 ± 16 Ma. These tourmalines occur within and along the margins of post-kinematic quartz veins, parallel to the foliation fabric and marks the end stage of high temperature tectono-thermal events within the Illaara Greenstone Belt. The retention of 2935 ± 9 Ma tourmaline ages within the Illaara Greenstone Belt shows that the K/Ar system of tourmaline remained closed throughout repeated upper-greenschist metamorphic events (∼450 °C) between the ages of c.a. 2930 to 2630 Ma in contrast to muscovite recording plateau ages of about 2600 Ma. This is in agreement with an approximate Ar closure temperature between ∼534 and 628 °C experimentally determined in this study.

Background: Breast cancer in the United States is diagnosed in over 90% of cases prior to evidence of distant metastasis (stages I–III) with approximately 70% of these cases classified as hormone receptor positive human epidermal growth factor receptor 2 negative (HR+HER2-).1 Despite primary surgery, radiation, and adjuvant endocrine/chemotherapy treatment options, approximately 20-30% of patients will experience relapse with distant metastases.2 Some clinical and pathological characteristics are known to be prognostic factors, but there are no standard definitions associated with level of risk. The objective of this study was to determine the extent of mortality associated with clinical and pathological characteristics of early breast cancer (EBC) using real-world data. Methods: Eligible patients from 2010–2016 Surveillance, Epidemiology, and End Results (SEER) data were aged ≥18 years and had a diagnosis of stage I, II, or III breast cancer with no distant metastases. Patients with HR-HER2- breast cancer were excluded. Mortality rates (95% confidence interval) by HER2 status and, for HR+HER2- tumors, by cancer stage, Bloom-Richardson (BR) grade, ipsilateral auxiliary lymph nodes status, and tumor size were estimated using Kaplan-Meier methods. Results: A total of 257,278 breast cancer patients were included: 214,578 HR+HER2-, 30,122 HR+HER2+, and 12,578 HR-HER2+. Mean age was 61.5 years, 99.1% were female, and 70.1% were white/non-Hispanic. The 5-year mortality rates were similar for HR+HER2- (12.3%) and HR+HER2+ (12.2%), whereas HR-HER2+ was numerically higher (16.8%). Within the HR+HER2- group, the 5-year mortality rates for subgroups are shown in Table 1. The highest mortality rate for both the node positive and micrometastases subgroups was approximately 30% for those who had 1–3 ipsilateral auxiliary lymph nodes, BR grade 3, and tumor size ≥5 cm. Conclusions: Patients with HR+HER2- EBC had similar mortality rates to patients with HR+HER2+ EBC. In patients with HR+HER2- EBC, higher mortality rates were numerically associated with ≥4 positive lymph nodes, BR grade 3, and greater tumor size. The effect on mortality was compounded with combinations of these histopathologic characteristics. References: 1. Howlander N, et al. J Natl Cancer Inst 2014;106:dju055; 2. Cardoso F, et al. Breast 2018;39:131-8. Table 1. Kaplan-Meier 5-year mortality estimates for patients with HR+HER2- early breast cancer by stage, grade, nodal status, and tumor size Node positiveN1mi: micrometastasesNode negativen=50,321n=10,096n=154,161 Mortality rate, % (95% CI)Mortality rate, % (95% CI)Mortality rate, % (95% CI)Overall18.15 (17.70–18.60)10.31 (9.51–11.11)10.54 (10.33–10.74)Stage INA7.29 (6.39–8.20)8.35 (8.13–8.56)Stage II12.56 (12.06–13.06)13.39 (11.91–14.87)16.69 (16.17–17.21)Stage III26.41 (25.61–27.22)19.10 (15.13–23.07)44.46 (40.69–48.23)1–3 Ips Ax nodes positive12.93 (12.43–13.43)9.96 (9.14–10.78)NA≥4 Ips Ax nodes positive24.75 (23.82–25.69)22.23 (15.64–28.82)NABR grade 325.62 (24.63–26.61)15.25 (13.09–17.41)14.24 (13.60–14.89)Tumor size Citation Format: Jacqueline Brown, Michael W Method, David R Nelson. Mortality rates associated with clinical and pathological characteristics of hormone receptor positive human epidermal growth factor receptor 2 negative early breast cancer: An analysis of the 2010-2016 surveillance, epidemiology, and end results data [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-08-18.

Species belonging to the bacterial phyla

Cytochrome P450 monooxygenases (CYPs/P450s) are heme thiolate proteins present in species across the biological kingdoms. By virtue of their broad substrate promiscuity and regio- and stereo-selectivity, these enzymes enhance or attribute diversity to secondary metabolites. Actinomycetes species are well-known producers of secondary metabolites, especially

We report our investigation of the utility of peptide crosslinking cytochrome P450 enzymes from biarylitide biosynthesis to generate a range of cyclic tripeptides from simple synthons. The crosslinked tripeptides produced by this P450 include both tyrosine-histidine (A-N-B) and tyrosine-tryptophan (A-O-B) crosslinked tripeptides, the latter a rare example of a phenolic crosslink to an indole moiety. Tripeptides are easily isolated following proteolytic removal of the leader peptide and can incorporate a wide range of amino acids in the residue inside the crosslinked tripeptide. Given the utility of peptide crosslinks in important natural products and the synthetic challenge that these can represent, P450 enzymes have the potential to play roles as important tools in the generation of high-value cyclic tripeptides for incorporation in synthesis, which can be yet further diversified using selective chemical techniques through specific handles contained within these tripeptides.

For the last six decades, cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, have been under the spotlight due to their regio- and stereo-selective oxidation activities, which has led to the exploration of their applications in almost all known areas of biology. The availability of many genome sequences allows us to understand the evolution of P450s in different organisms, especially in the Bacteria domain. The phenomenon that "P450s play a key role in organisms' adaptation vis a vis lifestyle of organisms impacts P450 content in their genome" was proposed based on studies on a handful of individual bacterial groups. To have conclusive evidence, one must analyze P450s and their role in secondary metabolism in species with diverse lifestyles but that belong to the same category. We selected species of the phylum

Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study’s results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.

Multiple real-world studies have confirmed the safety and efficacy of hepatitis C (HCV) direct-acting antivirals (DAAs); however, few studies have provided data on long-term outcomes of patients without cirrhosis after achieving sustained virologic response (SVR).

We investigate the ground state configurations of $p$-atic liquid crystals on fixed curved surfaces. We focus on the intrinsic geometry and show that isothermal coordinates are particularly convenient as they explicitly encode a geometric contribution to the elastic potential. In the special case of a cone with half-angle $\beta$, the apex develops an effective topological charge of $-\chi$, where $2\pi\chi = 2\pi(1-\sin\beta)$ is the deficit angle of the cone, and a topological defect of charge $\sigma$ behaves as if it had an effective topological charge $Q_\mathrm{eff} = (\sigma - \sigma^2/2)$ when interacting with the apex. The effective charge of the apex leads to defect absorption and emission at the cone apex as the deficit angle of the cone is varied. For total topological defect charge 1, e.g. imposed by tangential boundary conditions at the edge, we find that for a disk the ground state configuration consists of $p$ defects each of charge $+1/p$ lying equally spaced on a concentric ring of radius $d = (\frac{p-1}{3p-1})^{\frac{1}{2p}} R$, where $R$ is the radius of the disk. In the case of a cone with tangential boundary conditions at the base, we find three types of ground state configurations as a function of cone angle: (1) for sharp cones, all of the $+1/p$ defects are absorbed by the apex; (2) at intermediate cone angles, some of the $+1/p$ defects are absorbed by the apex and the rest lie equally spaced along a concentric ring on the flank; and (3) for nearly flat cones, all of the $+1/p$ defects lie equally spaced along a concentric ring on the flank. Here the defect positions and the absorption transitions depend intricately on $p$ and the deficit angle which we analytically compute. We check these results with numerical simulations for a set of commensurate cone angles and find excellent agreement., Comment: 12 + 11 pages, 10 figures

Antagonistic interactions are widespread in the microbial world and affect microbial evolutionary dynamics. Natural microbial communities often display spatial structure, which affects biological interactions, but much of what we know about microbial antagonism comes from laboratory studies of well-mixed communities. To overcome this limitation, we manipulated two killer strains of the budding yeast Saccharomyces cerevisiae, expressing different toxins, to independently control the rate at which they released their toxins. We developed mathematical models that predict the experimental dynamics of competition between toxin-producing strains in both well-mixed and spatially structured populations. In both situations, we experimentally verified theory’s prediction that a stronger antagonist can invade a weaker one only if the initial invading population exceeds a critical frequency or size. Finally, we found that toxin-resistant cells and weaker killers arose in spatially structured competitions between toxin-producing strains, suggesting that adaptive evolution can affect the outcome of microbial antagonism in spatial settings.

Metabolic models are reconstructed based on an organism's available genome annotation and provide predictive tools to study metabolic processes at a systems-level. Genome-scale metabolic models may include gaps as well as reactions that are unverified experimentally. Reconstructed models of newly isolated microalgal species will result in weaknesses due to these gaps, as there is usually sparse biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology is an effective, high-throughput method that functionally determines cellular metabolic activities in response to a wide array of entry metabolites. Combining the high throughput phenotypic assays with metabolic modeling can allow existing metabolic network models to be rapidly reconstructed or optimized by providing biochemical evidence to support and expand genomic evidence. This work will show the use of PM assays for the study of microalgae by using the green microalgal model species Chlamydomonas reinhardtii as an example. Experimental evidence for over 254 reactions obtained by PM was used in this study to expand and refine a genome-scale C. reinhardtii metabolic network model, iRC1080, by approximately 25 percent. The protocol created here can be used as a basis for functionally profiling the metabolism of other microalgae, including known microalgae mutants and new isolates.

The birth-and-death model of multigene family evolution describes how families can expand by duplication and contract by gene deletion and formation of pseudogenes. The phylogenetic stability of a gene is thought to be related to the degree of functional importance. However, it is unclear how much evolution of a gene in a gene family is driven by adaptive versus neutral processes. The cytochrome P450s are one of the most diverse and well-studied multigene families, involved in both physiological and xenobiotic functions. Bees have a high toxin exposure due to their diet of nectar and pollen, as well as the resin-collecting behavior exhibited by some bees. Here, we describe the P450s of the orchid bee Euglossa dilemma. Orchid bees are a neotropical clade in which males form perfume bouquets used in courtship displays by collecting a diverse set of volatile compounds, resulting in high chemical compound exposure. We conducted phylogenetic and selection analyses across ten bee species encompassing three bee families. We do not find a relationship between the ecology of a bee species and its P450 repertoire. Our analyses reveal that P450 clades can be classified into stable and unstable clades, and that genes involved in xenobiotic metabolism are more likely to belong to unstable clades. Furthermore, we find that unstable clades are under more dynamic evolutionary pressures, with signals of adaptive evolution detected, suggesting that both gene duplication and positive selection driving sequence divergence have played a role in the diversification of bee P450s. Our works highlights the complexity of multigene family evolution which does not always follow generalized predictions.Significance statementGene family evolution is characterized by deletion and duplication, but it is unclear if this is driven by adaptive or neutral evolutionary processes. To investigate the dynamics of gene family evolution we analyze the P450s of ten bee species, a well-studied gene family involved in both physiological and detoxification roles. We find that genes involved in detoxification are more likely to belong to unstable clades, exhibit dynamic evolutionary pressures, and show signals of adaptive evolution. However, we do not find evidence for a relationship between resin collection or sociality, and the P450 repertoire of a bee species. Our findings highlight the complexity of multigene family evolution which does not always follow generalized predictions.

The dynamics of a population expanding into unoccupied habitat has been primarily studied for situations in which growth and dispersal parameters are uniform in space or vary in one dimension. Here we study the influence of finite-sized individual inhomogeneities and their collective effect on front speed if randomly placed in a two-dimensional habitat. We use an individual-based model to investigate the front dynamics for a region in which dispersal or growth of individuals is reduced to zero (obstacles) or increased above the background (hotspots), respectively. In a regime where front dynamics is determined by a local front speed only, a principle of least time can be employed to predict front speed and shape. The resulting analytical solutions motivate an event-based algorithm illustrating the effects of several obstacles or hotspots. We finally apply the principle of least time to large heterogeneous environments by solving the Eikonal equation numerically. Obstacles lead to a slow-down that is dominated by the number density and width of obstacles, but not by their precise shape. Hotspots result in a speedup, which we characterise as function of hotspot strength and density. Our findings emphasise the importance of taking the dimensionality of the environment into account., Comment: Authors Wolfram M\"obius and Francesca Tesser contributed equally

We report the draft genome sequence for Pseudoalteromonas sp. strain JC3, an isolate obtained from an aquaculture facility for whiteleg shrimp ( Litopenaeus vannamei ). The JC3 genome suggests multiple mechanisms for microbial interactions, including a type VI secretion system and potential for antibiotic production.

BACKGROUND: The prevalence and risk factors for non-adherence to direct-acting antivirals (DAAs) for chronic hepatitis C virus (HCV) in clinical practice settings are under-studied. OBJECTIVES: (1) To quantify DAA non-adherence in the total cohort and among subgroups with and without mental health conditions, alcohol use, and substance use, and (2) to investigate patient- and treatment-level risk factor non-adherence. DESIGN: Prospective, observational cohort study. PARTICIPANTS: A total of 1562 patients receiving DAAs between January 2016 and October 2017 at 11 US medical centers including academic and community practices. MAIN MEASURES: Self-reported medication non-adherence, defined as any missed doses in the past 7 days, surveyed early (T2: at 4 ± 2 weeks) and late in treatment (T3: 2–3 weeks prior to end of treatment). Non-adherence to post-treatment follow-up visits was defined as absence of lab results after DAA therapy completion. KEY RESULTS: Of 1447 patients, 162 (11%) reported non-adherence at T2 or T3. Medical records indicated 262 (17%) of the 1562 participants had not returned for post-treatment visits. At baseline, 37% of patients reported mental health conditions, 15% reported alcohol use, and 23% reported using substances in the previous year. Baseline characteristics associated with DAA non-adherence included alcohol use (OR 1.96), younger age (< 35 years vs. > 55 years: OR 3.40), non-white race (OR > 2.26), and DAA treatment cohort, but not substance use or mental health condition. Non-adherence to follow-up exhibited association with younger age and a higher baseline overall symptom burden. Among 1287 patients with evaluable sustained virologic response (SVR) data, 53 patients (4%) did not achieve SVR. The bivariate correlation between adherence and SVR was negligible (r = 0.01). CONCLUSIONS: DAA non-adherence was low and SVR rates were high. Mental health conditions, substance use, and alcohol use should not disqualify patients from DAA therapy. Patients with alcohol use disorder before DAA therapy initiation may benefit from targeted on-treatment support. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11606-019-05394-9) contains supplementary material, which is available to authorized users.

Microalgae have been investigated for the photosynthetic production of natural products with industrial and biomedical applications. Their rapid growth offers an advantage over higher plants, while their complex metabolic capacities allow for the production of various molecules. Despite their potentials, molecular techniques are underdeveloped in microalgae compared to higher plants, fungi, and bacteria. However, recent advances in genome sequencing, strain development, and genome editing technologies, are providing thrust to enhance research on microalgal species that have branched out from several focal model organisms to encompass a great diversity of species. In this review, we highlight the recent, significant advances in microalgal research, with a focus on the development of new resources that can enhance work on model and non-model species.

Frankia bacteria are nitrogen fixing species from the Actinobacterium phylum which live on the root nodules of plants. They have been hypothesised to have significant potential for natural product biosynthesis. The cytochrome P450 monooxygenase complement of Frankia sp. EuI1c (Frankia inefficax sp.), which comprises 68 members, was analysed. Several members belonged to previously uncharacterised bacterial P450 families. There was an unusually high number of CYP189 family members (21) suggesting that this family has undergone gene duplication events which are classified as "blooms". The likely electron transfer partners for the P450 enzymes were also identified and analysed. These consisted of predominantly [3Fe-4S] cluster containing ferredoxins (eight), a single [2Fe-2S] ferredoxin and a couple of ferredoxin reductases. Three of these CYP family members were produced and purified, using Escherichia coli as a host, and their substrate range was characterised. CYP1027H1 and CYP150A20 bound a broad range of norisoprenoids and terpenoids. CYP1074A2 was highly specific for certain steroids including testosterone, progesterone, stanolone and 4-androstene-3,17-dione. It is likely that steroids are the physiological substrates of CYP1074A2. These results also give an indication that terpenoids are the likely substrates of CYP1027H1 and CYP150A2. The large number of P450s belonging to distinct families as well as the associated electron transfer partners found in different Frankia strains highlights the importance of this family of enzymes has in the secondary metabolism of these bacteria.

BACKGROUND: 50% of liver cancer is caused by hepatitis C virus (HCV). Baby boomers are at increased risk and are recommended for one-time HCV screening. However

Patients infected with hepatitis C virus (HCV) treated with interferon‐free direct‐acting antivirals may still require ribavirin. However, ribavirin is associated with adverse events that can limit its use. This open‐label, multicentre, Phase 3 study evaluated the safety and efficacy of ombitasvir/paritaprevir/ritonavir + dasabuvir (OBV/PTV/r + DSV) with low‐dose ribavirin for 12 weeks in genotype 1a‐infected patients without cirrhosis. The primary efficacy endpoint was sustained virologic response at post‐treatment Week 12 (SVR12). The primary safety endpoint was haemoglobin

The Cytochrome P450 gene family is one of the largest in plants. Cytochrome P450 sequences have been annotated in the Saccharum spontaneum genome and they make up 1.3% of the known alleles. 394 genes have been identified in this family after mining two releases of the S. spontaneum AP85–441 genome. The P450 sequences are most similar to those of sorghum. The 45 CYP families in sugarcane have been compared to sorghum P450s. CYP51 was the most similar sequence at 98.6%. Average percent identity to the best plant blast match was 86%. Three of the 45 CYP families show modest gene expansion. CYP71 has 15 more genes CYP76 has 12 more genes and CYP81 has 6 more genes than sorghum. The other families are identical or within 4 genes, showing a strong similarity between P450s in the two species. Alleles have been assigned for this tetraploid genome. Only 32% of the genes still have four alleles.

There are limiteddata on long-term changes in the gut microbiome after acute lymphoblastic leukemia (ALL) therapy. We compared the gut microbial composition in stool samples of nine survivors of childhood ALL with 10 healthy sibling controls using 16S rRNA gene sequencing. Analysis of beta diversity within family units demonstrated a significant difference in bacterial strains between patients and healthy siblings. A significant difference in alpha diversity between patients and their healthy siblings was noted using Pielou's evenness. The composition of the gut microbiome differs between pediatric ALL survivors and healthy sibling controls for years after completion of therapy.

Background and aims Multiple direct-acting antiviral (DAA) regimens are available to treat HCV genotype 1 infection. However, comparative effectiveness from randomized controlled trials of DAA regimens is unavailable. Approach and results We conducted a pragmatic randomized controlled trial (NCT02786537) to compare the effectiveness of DAAs for HCV genotype 1a or 1b on viral response, safety, tolerability, and medication nonadherence. Adults with compensated liver disease, HCV genotype 1, not pregnant or breastfeeding, and with health insurance likely to cover ledipasvir/sofosbuvir (LDV/SOF) were recruited from 34 US viral hepatitis clinics. Participants were randomized (± ribavirin) to LDV/SOF, elbasvir/grazoprevir (EBR/GZR), and paritaprevir/ritonavir/ombitasvir+dasabuvir (PrOD; treatment arm stopped early). Primary outcomes included sustained viral response at 12 weeks (SVR12), clinician-recorded adverse events, patient-reported symptoms, and medication nonadherence. Between June 2016 and March 2018, 1,609 participants were randomized. Among 1,128 participants who received ≥1 dose of EBR/GZR or LDV/SOF (± ribavirin), SVR12 was 95.2% (95% CI, 92.8%-97.6%) and 97.4% (95% CI, 95.5%-99.2%), respectively, with a difference estimate of 2.2% (-0.5% to 4.7%), falling within the "equivalence" interval (-5% to 5%). While most (56%) participants experienced adverse events, few were serious (4.2%) or severe (1.8%). In the absence of ribavirin, discontinuations due to adverse events were rare. Patient-reported symptoms and medication nonadherence were similar. Study limitations were dropout due to insurance denial and loss to follow-up after treatment, limiting the ability to measure SVR12. Conclusions This pragmatic trial demonstrated high SVR12 for participants treated with EBR/GZR and LDV/SOF with few adverse effects. Overall, the two regimens were equivalent in effectiveness. The results support current HCV guidelines that do not distinguish between ribavirin-free EBR/GZR and LDV/SOF.

Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.

Vibrio coralliilyticus is an extracellular bacterial pathogen and a causative agent of vibriosis in larval oysters. Host mortality rates can quickly reach 100% during vibriosis outbreaks in oyster hatcheries. Type VI Secretion Systems (T6SS) are rapidly polymerizing, contact dependent injection apparatus for prey cell intoxication and play important roles in pathogenesis. DNA sequencing of V. coralliilyticus RE22Sm indicated the likely presence of two functional T6SSs with one on each of two chromosomes. Here, we investigated the antibacterial and anti-eukaryotic roles of the two T6SSs (T6SS1 and T6SS2) against E. coli Sm10 cells and Crassostrea virginica larvae, respectively. Mutations in hcp and vgrG genes were created and characterized for their effects upon bacterial antagonism and eukaryotic host virulence. Mutations in hcp1 and hcp2 resulted in significantly reduced antagonism against E. coli Sm10, with the hcp2 mutation demonstrating the greater impact. In contrast, mutations in vgrG1 or vgrG2 had little effect on E. coli killing. In eastern oyster larval challenge assays, T6SS1 mutations in either hcp1 or vgrG1 dramatically attenuated virulence against C. virginica larvae. Strains with restored wild type hcp or vgrG genes reestablished T6SS-mediated killing to that of wild type V. coralliilyticus RE22Sm. These data suggest that the T6SS1 of V. coralliilyticus RE22Sm principally targets eukaryotes and secondarily bacteria, while the T6SS2 primarily targets bacterial cells and secondarily eukaryotes. Attenuation of pathogenicity was observed in all T6SS mutants, demonstrating the requirement for proper assembly of the T6SS systems to maintain maximal virulence.ImportanceVibriosis outbreaks lead to large-scale hatchery losses of oyster larvae (product and seed) where Vibrio sp. associated losses of 80 to 100 percent are not uncommon. Practical and proactive biocontrol measures can be taken to help mitigate larval death by Vibrio sp. by better understanding the underlying mechanisms of virulence in V. coralliilyticus. In this study, we demonstrate the presence of two Type VI Secretion Systems (T6SS) in V. coralliilyticus RE22Sm and interrogate the roles of each T6SS in bacterial antagonism and pathogenesis against a eukaryotic host. Specifically, we show that the loss of T6SS1 function results in the loss of virulence against oyster larvae.