Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity

Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.

Obesity and metabolic syndrome in patients with heart failure with preserved ejection fraction: a cross-sectional analysis of the Veradigm Cardiology Registry

BACKGROUND

The proportion of heart failure patients with preserved ejection fraction has been rising over the past decades and has coincided with increases in the prevalence of obesity and metabolic syndrome. The relationship between these interconnected comorbidities and heart failure with preserved ejection fraction (HFpEF) is still poorly understood. This study characterized obesity and metabolic syndrome among real-world patients with HFpEF.

METHODS

We identified adults with heart failure in the Veradigm Cardiology Registry, previously the PINNACLE Registry, with a left ventricular ejection fraction measurement ≥ 50% between 01/01/2016 and 12/31/2019. Patients were stratified by obesity diagnosis and presence of metabolic syndrome (≥ 3 of the following: diabetes, hypertension, hyperlipidemia, and obesity). We captured baseline demographic and clinical characteristics and used multivariable logistic regression to examine the odds of having cardiac (atrial fibrillation, coronary artery disease, coronary artery bypass surgery, myocardial infarction, and stroke/transient ischemic attack) and non-cardiac (chronic kidney disease, chronic liver disease, and peripheral artery disease) comorbidities of interest. The models adjusted for age and sex, and the main covariates of interest were obesity and metabolic burden score (0-3 based on the presence of diabetes, hypertension, and hyperlipidemia). The models were run with and without an obesity*metabolic burden score interaction term.

RESULTS

This study included 264,571 patients with HFpEF, of whom 55.7% had obesity, 52.5% had metabolic syndrome, 42.5% had both, and 34.3% had neither. After adjusting for age, sex, and burden of other metabolic syndrome-associated diagnoses, patients with HFpEF with obesity had lower odds of a diagnosis of other evaluated comorbidities relative to patients without obesity. The presence of metabolic syndrome in HFpEF appears to increase comorbidity burden as each additional metabolic syndrome-associated diagnosis was associated with higher odds of assessed comorbidities except atrial fibrillation.

CONCLUSION

Obesity was common among patients with HFpEF and not always co-occurring with metabolic syndrome. Multivariable analysis suggested that patients with obesity may develop HFpEF in the absence of other driving factors such as cardiovascular disease or metabolic syndrome.

Structure-Function Analysis of the Essential Mycobacterium tuberculosis P450 Drug Target, CYP121A1

Cytochrome P450 CYP121A1 is a well-known drug target against Mycobacterium tuberculosis, the human pathogen that causes the deadly disease tuberculosis (TB). CYP121A1 is a unique P450 enzyme because it uses classical and non-classical P450 catalytic processes and has distinct structural features among P450s. However, a detailed investigation of CYP121A1 protein structures in terms of active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 53 CYP121A1 crystal structures were investigated in this study. Critical amino acids required for CYP121A1's overall activity were identified and highlighted this enzyme's rigid architecture and substrate selectivity. The CYP121A1-fluconazole crystal structure revealed a novel azole drug-P450 binding mode in which azole heme coordination was facilitated by a water molecule. Fragment-based inhibitor approaches revealed that CYP121A1 can be inhibited by molecules that block the substrate channel or by directly interacting with the P450 heme. This study serves as a reference for the precise understanding of CYP121A1 interactions with different ligands and the structure-function analysis of P450 enzymes in general. Our findings provide critical information for the synthesis of more specific CYP121A1 inhibitors and their development as novel anti-TB drugs.

The roles of type 2 diabetes and obesity in disease activity and progression of non-alcoholic fatty liver disease/non-alcoholic steatohepatitis

OBJECTIVE

We examined the roles of type 2 diabetes (T2D) and obesity in disease activity and fibrosis progression/regression in patients with non-alcoholic fatty liver disease/non-alcoholic steatohepatitis (NAFLD/NASH).

METHODS

This multi-center, retrospective study included patients with suspected or histologically proven NAFLD/NASH from the NASH Clinical Research Network. Outcomes included disease activity and rate of fibrosis, assessed using liver-biopsy driven measures (NAFLD activity score [NAS] and fibrosis score [FS]). Logistic regression and doubly robu estimation of causal effects tested relationships among T2D, obesity, and NAFLD/NASH.

RESULTS

The analytical sample included 870 adult patients with baseline biopsy data and 157 patients with multiple biopsy data. Patients with NAFLD/NASH and T2D had significantly higher baseline average NAS (4.52 vs. 4.13; p = 0.009) and FS (2.17 vs. 1.56; p < 0.0001); those with T2D had a significantly greater reduction in average NAS over time (-0.77/year vs. -0.17/year; p = 0.0008). Change in FS over time did not differ significantly by T2D status (-0.23/year vs. -0.04/year; p = 0.34). Baseline NAS, baseline FS, and change in average NAS over time did not differ significantly by obesity status (4.17 vs. 4.47; p = 0.16; 1.73 vs.1.92; p = 0.31; -0.40/year vs. -0.59/year; p = 0.62, respectively). Patients with obesity had a slight increase in FS but those without obesity had a reduction in average FS over time (0.07/year vs. -0.27/year; p = 0.008).

CONCLUSIONS

Patients with NAFLD/NASH and T2D had greater baseline disease activity versus those without T2D, but there was greater regression of disease activity over time among those with T2D. Patients with NAFLD/NASH and obesity had worsening of fibrosis versus those without obesity. NCT00063622.

A cytochrome P450 insecticide detoxification mechanism is not conserved across the Megachilidae family of bees

Recent work has demonstrated that many bee species have specific cytochrome P450 enzymes (P450s) that can efficiently detoxify certain insecticides. The presence of these P450s, belonging or closely related to the CYP9Q subfamily (CYP9Q-related), is generally well conserved across the diversity of bees. However, the alfalfa leafcutter bee, Megachile rotundata, lacks CYP9Q-related P450s and is 170-2500 times more sensitive to certain insecticides than bee pollinators with these P450s. The extent to which these findings apply to other Megachilidae bee species remains uncertain. To address this knowledge gap, we sequenced the transcriptomes of four Megachile species and leveraged the data obtained, in combination with publicly available genomic data, to investigate the evolution and function of P450s in the Megachilidae. Our analyses reveal that several Megachilidae species, belonging to the Lithurgini, Megachilini and Anthidini tribes, including all species of the Megachile genus investigated, lack CYP9Q-related genes. In place of these genes Megachile species have evolved phylogenetically distinct CYP9 genes, the CYP9DM lineage. Functional expression of these P450s from M. rotundata reveal they lack the capacity to metabolize the neonicotinoid insecticides thiacloprid and imidacloprid. In contrast, species from the Osmiini and Dioxyini tribes of Megachilidae have CYP9Q-related P450s belonging to the CYP9BU subfamily that are able to detoxify thiacloprid. These findings provide new insight into the evolution of P450s that act as key determinants of insecticide sensitivity in bees and have important applied implications for pesticide risk assessment.

Structure-Function Analysis of the Biotechnologically Important Cytochrome P450 107 (CYP107) Enzyme Family

Cytochrome P450 monooxygenases (CYPs; P450s) are a superfamily of heme-containing enzymes that are recognized for their vast substrate range and oxidative multifunctionality. CYP107 family members perform hydroxylation and epoxidation processes, producing a variety of biotechnologically useful secondary metabolites. Despite their biotechnological importance, a thorough examination of CYP107 protein structures regarding active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 44 CYP107 crystal structures were investigated in this study. We demonstrate that the CYP107 active site cavity is very flexible, with ligand binding reducing the volume of the active site in some situations and increasing volume size in other instances. Polar interactions between the substrate and active site residues result in crucial salt bridges and the formation of proton shuttling pathways. Hydrophobic interactions, however, anchor the substrate within the active site. The amino acid residues within the binding pocket influence substrate orientation and anchoring, determining the position of the hydroxylation site and hence direct CYP107's catalytic activity. Additionally, the amino acid dynamics within and around the binding pocket determine CYP107's multifunctionality. This study serves as a reference for understanding the structure-function analysis of CYP107 family members precisely and the structure-function analysis of P450 enzymes in general. Finally, this work will aid in the genetic engineering of CYP107 enzymes to produce novel molecules of biotechnological interest.

Geometric frustration of hard-disk packings on cones

Conical surfaces pose an interesting challenge to crystal growth: A crystal growing on a cone can wrap around and meet itself at different radii. We use a disk-packing algorithm to investigate how this closure constraint can geometrically frustrate the growth of single crystals on cones with small opening angles. By varying the crystal seed orientation and cone angle, we find that-except at special commensurate cone angles-crystals typically form a seam that runs along the axial direction of the cone, while near the tip, a disordered particle packing forms. We show that the onset of disorder results from a finite-size effect that depends strongly on the circumference and not on the seed orientation or cone angle. This finite-size effect occurs also on cylinders, and we present evidence that on both cylinders and cones, the defect density increases exponentially as circumference decreases. We introduce a simple model for particle attachment at the seam that explains the dependence on the circumference. Our findings suggest that the growth of single crystals can become frustrated even very far from the tip when the cone has a small opening angle. These results may provide insights into the observed geometry of conical crystals in biological and materials applications.

Genome-Wide Analysis of the Cytochrome P450 Monooxygenases in the Lichenized Fungi of the Class Lecanoromycetes

Lichens are unique organisms that exhibit a permanent symbiosis between fungi and algae or fungi and photosynthetic bacteria. Lichens have been found to produce biotechnologically valuable secondary metabolites. A handful of studies showed that tailoring enzymes such as cytochrome P450 monooxygenases (CYPs/P450s) play a key role in synthesizing these metabolites. Despite the critical role of P450s in the biosynthesis of secondary metabolites, the systematic analysis of P450s in lichens has yet to be reported. This study is aimed to address this research gap. A genome-wide analysis of P450s in five lichens from the fungal class Lecanoromycetes revealed the presence of 434 P450s that are grouped into 178 P450 families and 345 P450 subfamilies. The study indicated that none of the P450 families bloomed, and 15 P450 families were conserved in all five Lecanoromycetes. Lecanoromycetes have more P450s and higher P450 family diversity compared to Pezizomycetes. A total of 73 P450s were found to be part of secondary metabolite gene clusters, indicating their potential involvement in the biosynthesis of secondary metabolites. Annotation of P450s revealed that CYP682BG1 and CYP682BG2 from Cladonia grayi and Pseudevernia furfuracea (physodic acid chemotype) are involved in the synthesis of grayanic acid and physodic acid, CYP65FQ2 from Stereocaulon alpinum is involved in the synthesis of atranorin, and CYP6309A2 from Cladonia uncialis is involved in the synthesis of usnic acid. This study serves as a reference for future annotation of P450s in lichens.

Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis

Horse chestnut (Aesculus chinensis) is an important medicinal tree that contains various bioactive compounds, such as aescin, barrigenol-type triterpenoid saponins (BAT), and aesculin, a glycosylated coumarin. Herein, we report a 470.02 Mb genome assembly and characterize an Aesculus-specific whole-genome duplication event, which leads to the formation and duplication of two triterpenoid biosynthesis-related gene clusters (BGCs). We also show that AcOCS6, AcCYP716A278, AcCYP716A275, and AcCSL1 genes within these two BGCs along with a seed-specific expressed AcBAHD6 are responsible for the formation of aescin. Furthermore, we identify seven Aesculus-originated coumarin glycoside biosynthetic genes and achieve the de novo synthesis of aesculin in E. coli. Collinearity analysis shows that the collinear BGC segments can be traced back to early-diverging angiosperms, and the essential gene-encoding enzymes necessary for BAT biosynthesis are recruited before the splitting of Aesculus, Acer, and Xanthoceras. These findings provide insight on the evolution of gene clusters associated with medicinal tree metabolites.

Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.

Pezizomycetes Genomes Reveal Diverse P450 Complements Characteristic of Saprotrophic and Ectomycorrhizal Lifestyles

Cytochrome P450 monooxygenases (CYPs/P450s) are heme proteins that play a role in organisms' primary and secondary metabolism. P450s play an important role in organism adaptation since lifestyle influences P450 composition in their genome. This phenomenon is well-documented in bacteria but less so in fungi. This study observed this phenomenon where diverse P450 complements were identified in saprophytic and ectomycorrhizal Pezizomycetes. Genome-wide data mining, annotation, and phylogenetic analysis of P450s in 19 Pezizomycetes revealed 668 P450s that can be grouped into 153 P450 families and 245 P450 subfamilies. Only four P450 families, namely, CYP51, CYP61, CYP5093, and CYP6001, are conserved across 19 Pezizomycetes, indicating their important role in these species. A total of 5 saprophyte Pezizomycetes have 103 P450 families, whereas 14 ectomycorrhizal Pezizomycetes have 89 P450 families. Only 39 P450 families were common, and 50 and 64 P450 families, respectively, were unique to ectomycorrhizal and saprophytic Pezizomycetes. These findings suggest that the switch from a saprophytic to an ectomycorrhizal lifestyle led to both the development of diverse P450 families as well as the loss of P450s, which led to the lowest P450 family diversity, despite the emergence of novel P450 families in ectomycorrhizal Pezizomycetes.

Aliens in the CYPome of the black fungus gnat, Bradysia coprophila

The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.

Active topological defect absorption by a curvature singularity

We leverage the Born-Oppenheimer approximation to present a general description of topological defects dynamics in $p$-atic materials on curved surfaces. Focusing on the case of an active nematic, we find that activity induces a geometric contribution to the motility of the $+1/2$ defect. Moreover, in the case of a cone, the simplest example of a geometry with curvature singularity, we find that the motility depends on the deficit angle of the cone and changes sign when the deficit angle is bigger than $\pi$, leading to the change in active behavior from contractile (extensile) to extensile (contractile) behavior. Using our analytical framework, we then identify for positively charged defects the basin of attraction to the cone apex and present closed-form predictions for defect trajectories near the apex. The analytical results are quantitatively corroborated against full numerical simulations, with excellent agreement when the capture radius is small compared to the cone size.

Gaps Remain for Achieving HbA1c Targets for People with Type 1 or Type 2 Diabetes Using Insulin: Results from NHANES 2009-2020

INTRODUCTION

Glycated hemoglobin A1c (HbA1c) is an important measure to assess glycemic control and predict diabetes complications. However, there is limited information on trends in HbA1c among people with diabetes (PwDs) who use insulin. The aim of this study was to describe trends in HbA1c among PwDs who use insulin by diabetes type and insulin regimen.

METHODS

A retrospective analysis was conducted using data from the National Health and Nutrition Examination Survey (NHANES, 2009-2020). PwDs were classified into three cohorts: type 1 diabetes mellitus (T1DM), type 2 diabetes mellitus using mealtime insulin (T2DM-MTI), and type 2 diabetes mellitus (T2DM) using basal-only insulin (T2DM basal-only). Trends in HbA1c over time were assessed using regression analysis after adjusting for age, gender, and race/ethnicity.

RESULTS

Mean HbA1c values aggregated over 2009-2020 were 8.0% (T1DM), 8.6% (T2DM-MTI), and 8.6% (T2DM basal-only). The American Diabetes Association-recommended target of HbA1c of < 7% was achieved by 25.2% of people in the T1DM and T2DM-MTI groups each and by 12.3% of people in the T2DM basal-only group. Over time, an upward trend was observed in the percentage of people achieving HbA1c < 7% in the T2DM basal-only group. The percentage of PwDs achieving individualized HbA1c targets was 27.0%, 12.4%, and 16.1% for the T1DM, T2DM-MTI, and T2DM basal-only groups, respectively.

CONCLUSIONS

Our study using NHANES data suggests that approximately 25% of PwDs achieve glycemic targets. This study highlights the need for improved therapies to better manage glycemic targets in PwDs.

Plant (di)terpenoid evolution: from pigments to hormones and beyond

Covering: up to 2014-2022.Diterpenoid biosynthesis in plants builds on the necessary production of (E,E,E)-geranylgeranyl diphosphate (GGPP) for photosynthetic pigment production, with diterpenoid biosynthesis arising very early in land plant evolution, enabling stockpiling of the extensive arsenal of (di)terpenoid natural products currently observed in this kingdom. This review will build upon that previously published in the Annual Review of Plant Biology, with a stronger focus on enzyme structure-function relationships, as well as additional insights into the evolution of (di)terpenoid metabolism since generated.

Trajectory of glycated haemoglobin over time, using real-world data, in type 2 diabetes patients with obesity on a U-100 basal-bolus insulin regimen

AIMS

To identify patient clusters with poor glucose control among type 2 diabetes mellitus (T2DM) patients with obesity who are receiving basal-bolus insulin and to identify the potential therapeutic inertia factors associated with poor control.

METHODS

Glycated haemoglobin (HbA1c) trajectories across a 3-year period were structured at 6-month intervals for a retrospective cohort of T2DM patients with obesity on basal-bolus insulin from the Veterans' Health Administration database. Based on each patient's longitudinal HbA1c features, an unsupervised clustering procedure was used to determine the numbers of clusters and associated trajectory patterns. Multinomial logistic regression was used to examine the association between HbA1c trajectory clusters and patient characteristics/treatment patterns.

RESULTS

A total of 51 273 patients were included, of whom 11.2% were in a subgroup with persistent missingness of HbA1c values. For those with sufficient HbA1c observations, cluster analysis indicated six distinct HbA1c trajectories: stable low (35.8%); stable high (20.8%); descending low (10.5%); ascending low (10.2%); descending high (5.7%); and ascending high (5.7%). Being of Black ethnicity, not initiating noninsulin antihyperglycaemic agents (sodium-glucose cotransporter-2 inhibitors, glucagon-like peptide-1 receptor agonists or thiazolidinediones) or concentrated insulin, low adherence (measured by proportion of days covered), and reduced insulin prescription refills were factors associated with poorer HbA1c clusters; similar factors were associated with persistent HbA1c missingness.

CONCLUSION

The present study found the potential for therapeutic inertia among a significant proportion of T2DM patients with obesity on basal-bolus insulin. Subgrouping T2DM patients based on HbA1c missingness and HbA1c trajectories can inform disease management strategies.

Development and Validation of Coding Algorithms to Identify Patients with Incident Non-Small Cell Lung Cancer in United States Healthcare Claims Data

Purpose

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.

Cytochrome P450 Blt Enables Versatile Peptide Cyclisation to Generate Histidine‐ and Tyrosine‐Containing Crosslinked Tripeptide Building Blocks

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.

Development of a claims-based flare algorithm for systemic lupus erythematosus

OBJECTIVE

To develop a claims-based algorithm identifying systemic lupus erythematosus (SLE) flares using a linked claims-electronic medical record (EMR) dataset.

METHODS

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.

RESULTS

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.

CONCLUSIONS

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.

Sustainable and equivalent improvements in symptoms and functional well-being following viral cure from ledipasvir/sofosbuvir versus elbasvir/grazoprevir for chronic hepatitis C infection: Findings from the randomized PRIORITIZE trial

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 of >3 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.

Spatial population genetics with fluid flow

The growth and evolution of microbial populations is often subjected to advection by fluid flows in spatially extended environments, with immediate consequences for questions of spatial population genetics in marine ecology, planktonic diversity and origin of life scenarios. Here, we review recent progress made in understanding this rich problem in the simplified setting of two competing genetic microbial strains subjected to fluid flows. As a pedagogical example we focus on antagonsim, i.e., two killer microorganism strains, each secreting toxins that impede the growth of their competitors (competitive exclusion), in the presence of stationary fluid flows. By solving two coupled reaction-diffusion equations that include advection by simple steady cellular flows composed of characteristic flow motifs in two dimensions (2D), we show how local flow shear and compressibility effects can interact with selective advantage to have a dramatic influence on genetic competition and fixation in spatially distributed populations. We analyze several 1D and 2D flow geometries including sources, sinks, vortices and saddles, and show how simple analytical models of the dynamics of the genetic interface can be used to shed light on the nucleation, coexistence and flow-driven instabilities of genetic drops. By exploiting an analogy with phase separation with nonconserved order parameters, we uncover how thesegeneticdrops harness fluid flows for novel evolutionary strategies, even in the presence of number fluctuations, as confirmed by agent-based simulations as well.

Defect absorption and emission for p-atic liquid crystals on cones

We investigate the ground-state configurations of two-dimensional liquid crystals with p-fold rotational symmetry (p-atics) 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 β, the apex develops an effective topological charge of -χ, where 2πχ=2π(1-sinβ) is the deficit angle of the cone, and a topological defect of charge σ behaves as if it had an effective topological charge Q_{eff}=(σ-σ^{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=(p-1/3p-1)^{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: (i) for sharp cones, all of the +1/p defects are absorbed by the apex; (ii) 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 (iii) 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.

Machine learning algorithms for predicting direct-acting antiviral treatment failure in chronic hepatitis C: An HCV-TARGET analysis

BACKGROUND AND AIMS

We aimed to develop and validate machine learning algorithms to predict direct-acting antiviral (DAA) treatment failure among patients with HCV infection.

APPROACH AND RESULTS

We used HCV-TARGET registry data to identify HCV-infected adults receiving all-oral DAA treatment and having virologic outcome. Potential pretreatment predictors (n = 179) included sociodemographic, clinical characteristics, and virologic data. We applied multivariable logistic regression as well as elastic net, random forest, gradient boosting machine (GBM), and feedforward neural network machine learning algorithms to predict DAA treatment failure. Training (n = 4894) and validation (n = 1631) patient samples had similar sociodemographic and clinical characteristics (mean age, 57 years; 60% male; 66% White; 36% with cirrhosis). Of 6525 HCV-infected adults, 95.3% achieved sustained virologic response, whereas 4.7% experienced DAA treatment failure. In the validation sample, machine learning approaches performed similarly in predicting DAA treatment failure (C statistic [95% CI]: GBM, 0.69 [0.64-0.74]; random forest, 0.68 [0.63-0.73]; feedforward neural network, 0.66 [0.60-0.71]; elastic net, 0.64 [0.59-0.70]), and all four outperformed multivariable logistic regression (0.51 [0.46-0.57]). Using the Youden index to identify the balanced risk score threshold, GBM had 66.2% sensitivity and 65.1% specificity, and 12 individuals were needed to evaluate to identify 1 DAA treatment failure. Over 55% of patients with treatment failure were classified by the GBM in the top three risk decile subgroups (positive predictive value: 6%-14%). The top 10 GBM-identified predictors included albumin, liver enzymes (aspartate aminotransferase, alkaline phosphatase), total bilirubin levels, sex, HCV viral loads, sodium level, HCC, platelet levels, and tobacco use.

CONCLUSIONS

Machine learning algorithms performed effectively for risk prediction and stratification of DAA treatment failure.

Fractional defect charges in liquid crystals with p-fold rotational symmetry on cones

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.

An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species

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 Salinispora species. Despite the importance of P450s, a comprehensive comparative analysis of P450s and their role in secondary metabolism in Salinispora species is not reported. We therefore analyzed P450s in 126 strains from three different species Salinispora arenicola, S. pacifica, and S. tropica. The study revealed the presence of 2643 P450s that can be grouped into 45 families and 103 subfamilies. CYP107 and CYP125 families are conserved, and CYP105 and CYP107 families are bloomed (a P450 family with many members) across Salinispora species. Analysis of P450s that are part of secondary metabolite biosynthetic gene clusters (smBGCs) revealed Salinispora species have an unprecedented number of P450s (1236 P450s-47%) part of smBGCs compared to other bacterial species belonging to the genera Streptomyces (23%) and Mycobacterium (11%), phyla Cyanobacteria (8%) and Firmicutes (18%) and the classes Alphaproteobacteria (2%) and Gammaproteobacteria (18%). A peculiar characteristic of up to six P450s in smBGCs was observed in Salinispora species. Future characterization Salinispora species P450s and their smBGCs have the potential for discovering novel secondary metabolites.

Pathogen-induced biosynthetic pathways encode defense-related molecules in bread wheat

Wheat is a widely grown food crop that suffers major yield losses due to attack by pests and pathogens. A better understanding of biotic stress responses in wheat is thus of major importance. The recently assembled bread wheat genome coupled with extensive transcriptomic resources provides unprecedented new opportunities to investigate responses to pathogen challenge. Here, we analyze gene coexpression networks to identify modules showing consistent induction in response to pathogen exposure. Within the top pathogen-induced modules, we identify multiple clusters of physically adjacent genes that correspond to six pathogen-induced biosynthetic pathways that share a common regulatory network. Functional analysis reveals that these pathways, all of which are encoded by biosynthetic gene clusters, produce various different classes of compounds—namely, flavonoids, diterpenes, and triterpenes, including the defense-related compound ellarinacin. Through comparative genomics, we also identify associations with the known rice phytoalexins momilactones, as well as with a defense-related gene cluster in the grass model plant Brachypodium distachyon. Our results significantly advance the understanding of chemical defenses in wheat and open up avenues for enhancing disease resistance in this agriculturally important crop. They also exemplify the power of transcriptional networks to discover the biosynthesis of chemical defenses in plants with large, complex genomes.

Breast cancer-specific mortality in early breast cancer as defined by high-risk clinical and pathologic characteristics

OBJECTIVES

To investigate breast cancer-specific mortality by early breast cancer (EBC; Stages I-IIIC) subtype; incidence of high-risk indicators for recurrence (defined in monarchE trial); and mortality risk difference by those who did/did not meet these criteria.

MATERIALS AND METHODS

Analyses included patients with initial EBC diagnosis between 2010-2015 from Surveillance, Epidemiology, and End Results (SEER) data (n = 342,149). Cox proportional hazards models and Kaplan-Meier estimates examined mortality among 228,031 patients, by subtype (hormone receptor [HR]-positive [+], human epidermal growth factor receptor-2 [HER2] negative [-]; triple negative [TNBC]; HR+, HER2+; HR-, HER2+). Incidence and mortality among patients who did/did not meet monarchE clinicopathological high-risk criteria were examined.

RESULTS

Among patients with HR+, HER2- EBC, histologic Grade 3 (vs. Grade 1) was the most influential factor on mortality (hazard ratio, 3.61; 95%CI, 3.27, 3.98). Among patients with TNBC, ≥4 ipsilateral axillary positive nodes (vs. node negative) was the most influential factor on mortality (hazard ratio, 3.46; 95%CI, 2.87, 4.17). For patients with HR-, HER2+ or HR+, HER2+ EBC, tumor size ≥5 cm (vs. <1 cm) and ≥4 ipsilateral axillary positive nodes were the most influential factors on mortality. The 60-month mortality rate for the 12% of patients within the HR+, HER2- EBC group meeting monarchE clinicopathological high-risk criteria was 16.5%, versus 7.0% (Stage II-III and node positive) and 2.8% (Stage I or node negative) for those not meeting criteria. The 60-month mortality rate for patients with TNBC was 18.5%.

CONCLUSION

Mortality risk and the relative importance of risk factors varied by subtype. monarchE clinicopathological high-risk criteria were associated with increased mortality risk among patients with HR+, HER2- EBC. Patients with HR+, HER2- EBC, and monarchE clinicopathological high-risk criteria experienced risk of mortality similar to patients with early TNBC. These data highlight a high unmet need in this select patient population who may benefit most from therapy escalation.

Anomalous Thermal Expansion in Ising-like Puckered Sheets

Motivated by efforts to create thin nanoscale metamaterials and understand atomically thin binary monolayers, we study the finite temperature statistical mechanics of arrays of bistable buckled dilations embedded in free-standing two-dimensional crystalline membranes that are allowed to fluctuate in three dimensions. The buckled nodes behave like discrete, but highly compressible, Ising spins, leading to a phase transition at T_{c} with singularities in the staggered "magnetization," susceptibility, and specific heat, studied via molecular dynamics simulations. Unlike conventional Ising models, we observe a striking divergence and sign change of the coefficient of thermal expansion near T_{c} caused by the coupling of flexural phonons to the buckled spin texture. We argue that a phenomenological model coupling Ising degrees of freedom to the flexural phonons in a thin elastic sheet can explain this unusual response.

Thermalized buckling of isotropically compressed thin sheets

The buckling of thin elastic sheets is a classic mechanical instability that occurs over a wide range of scales. In the extreme limit of atomically thin membranes like graphene, thermal fluctuations can dramatically modify such mechanical instabilities. We investigate here the delicate interplay of boundary conditions, nonlinear mechanics, and thermal fluctuations in controlling buckling of confined thin sheets under isotropic compression. We identify two inequivalent mechanical ensembles based on the boundaries at constant strain (isometric) or at constant stress (isotensional) conditions. Remarkably, in the isometric ensemble, boundary conditions induce a novel long-ranged nonlinear interaction between the local tilt of the surface at distant points. This interaction combined with a spontaneously generated thermal tension leads to a renormalization group description of two distinct universality classes for thermalized buckling, realizing a mechanical variant of Fisher-renormalized critical exponents. We formulate a complete scaling theory of buckling as an unusual phase transition with a size-dependent critical point, and we discuss experimental ramifications for the mechanical manipulation of ultrathin nanomaterials.

Do patients at high risk for Hepatitis C receive recommended testing? A retrospective cohort study of statewide Medicaid claims linked with OneFlorida clinical data

ABSTRACT

Hepatitis C virus (HCV) infection is a leading risk factor for hepatocellular carcinoma.We employed a retrospective cohort study design and analyzed 2012-2018 Medicaid claims linked with electronic health records data from the OneFlorida Data Trust, a statewide data repository containing electronic health records data for 15.07 million Floridians from 11 health care systems. Only adult patients at high-risk for HCV (n = 30,113), defined by diagnosis of: HIV/AIDS (20%), substance use disorder (64%), or sexually transmitted infections (22%) were included. Logistic regression examined factors associated with meeting the recommended sequence of HCV testing.Overall, 44.1% received an HCV test. The odds of receiving an initial test were significantly higher for pregnant females (odds ratio [OR]1.99; 95% confidence interval [CI] 1.86-2.12; P < .001) and increased with age (OR 1.01; 95% CI 1.00-1.01; P < .001).Among patients with low Charlson comorbidity index (CCI = 1), non-Hispanic (NH) black patients (OR 0.86; 95% CI 0.81-0.9; P < .001) had lower odds of getting an HCV test; however, NH black patients with CCI = 10 had higher odds (OR 1.41; 95% CI 1.21-1.66; P < .001) of receiving a test. Of those who tested negative during initial testing, 17% received a second recommended test after 6 to 24 months. Medicaid-Medicare dual eligible patients, those with high CCI (OR 1.14; 95% CI 1.11-1.17; P < .001), NH blacks (OR 1.93; 95% CI 1.61-2.32; P < .001), and Hispanics (OR 1.49; 95% CI 1.08-2.06; P = .02) were significantly more likely to have received a second HCV test, while pregnant females (OR 0.71; 95% CI 0.57-0.89; P = .003), had lower odds of receiving it. The majority of patients who tested positive during the initial test (97%) received subsequent testing.We observed suboptimal adherence to the recommended HCV testing among high-risk patients underscoring the need for tailored interventions aimed at successfully navigating high-risk individuals through the HCV screening process. Future interventional studies targeting multilevel factors, including patients, clinicians and health systems are needed to increase HCV screening rates for high-risk populations.

Antagonism between killer yeast strains as an experimental model for biological nucleation dynamics

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.

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

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.

Phonon eigenfunctions of inhomogeneous lattices: Can you hear the shape of a cone?

We study the phonon modes of interacting particles on the surface of a truncated cone resting on a plane subject to gravity, inspired by recent colloidal experiments. We derive the ground-state configuration of the particles under gravitational pressure in the small-cone-angle limit and find an inhomogeneous triangular lattice with spatially varying density but robust local order. The inhomogeneity has striking effects on the normal modes such that an important feature of the cone geometry, namely its apex angle, can be extracted from the lattice excitations. The shape of the cone leads to energy crossings at long wavelengths and frequency-dependent quasilocalization at short wavelengths. We analytically derive the localization domain boundaries of the phonons in the limit of small cone angle and check our results with numerical results for eigenfunctions.

HCV testing: Order and completion rates among baby boomers obtaining care from seven health systems in Florida, 2015-2017

Many U.S. residents infected with hepatitis C virus (HCV) are baby boomers (born 1945-1965), who remain undiagnosed. Past CDC and USPSTF guidelines recommended one-time HCV testing for all baby boomers, with newer guidelines recommending universal screening for all adults. This retrospective cohort study examined electronic medical records for patient visits from 2015 to 2017 within the OneFlorida Data Trust and University of South Florida Health system. We assessed percentages of HCV tests ordered and completed across four age groups (those born before 1945, 1945-1965, 1966-1985, and after 1985). In 2019, we used logistic regression to examine factors associated with HCV test ordering and completion among baby boomers, including age, race, sex, number of primary care visits, HIV status, hepatitis diagnosis, and liver cancer history. All age groups had low rates of HCV test orders. 4.4% of baby boomers had a test ordered in 2015, and 6.7% in 2016. Of those, 94.5% and 89.7% completed testing, respectively. All other races/ethnicities had lower likelihood of testing completion than Whites (Blacks (aOR 0.82, 95%, CI 0.75-0.91); Asians (0.69, 0.52-0.92); Hispanics (0.29, 0.26-0.32)), although test orders were higher for Asians (1.48, 1.37-1.61) and Blacks (1.78, 1.73-1.82). Tests ordered (11.42, 10.94-11.92) and completed (2.25, 1.94-2.60) were more likely among those with hepatitis history. Test orders were more likely for HIV-positive patients (3.68, 3.45-3.93), but completion was less likely (0.67, 0.57-0.78). Interventions are needed to increase testing rates so that HCV infections are treated early, mitigating HCV-related morbidity and mortality, especially related to liver cancer.

A Pragmatic, Randomized Controlled Trial of Oral Antivirals for the Treatment of Chronic Hepatitis C: The PRIORITIZE Study

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.

The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees

The birth-and-death model of multigene family evolution describes how gene families evolve and diversify through duplication and deletion. The cytochrome P450s are one of the most diverse and well-studied multigene families, involved in both physiological and xenobiotic functions. Extensive studies of insect P450 genes have demonstrated their role in insecticide resistance. Bees are thought to experience toxin exposure through their diet of nectar and pollen, as well as the resin-collecting behavior exhibited by some species. Here, we describe the repertoire of P450 genes in the orchid bee Euglossa dilemma. Male orchid bees form perfume bouquets used in courtship displays by collecting volatile compounds, resulting in exposure to compounds known to be toxic. In addition, we conducted phylogenetic and selection analyses across ten bee species encompassing three bee families. We find that social behavior and resin collection are not correlated with the repertoire of P450 present in a bee species. However, our analyses revealed that P450 clades can be classified as stable and unstable, 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 and exhibit signals of adaptive evolution. This work highlights the complexity of multigene family evolution, revealing that multiple factors contribute to the diversification, stability, and dynamics of this gene family. Furthermore, we provide a resource for future detailed studies investigating the function of different P450s in economically important bee species.

The collective effect of finite-sized inhomogeneities on the spatial spread of populations in two dimensions

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 speed-up, which we characterize as function of hotspot strength and density. Our findings emphasize the importance of taking the dimensionality of the environment into account.

Linkage of resistance-associated substitutions in GT1 sofosbuvir + NS5A inhibitor failures treated with glecaprevir/pibrentasvir

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-naïve. 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.

Protocol to generate and characterize biofouling transformants of a model marine diatom

Diatoms are a major group of microalgae that initiate biofouling by surface colonization of human-made underwater structures; however, the involved regulatory pathways remain uncharacterized. Here, we describe a protocol for identifying and validating regulatory genes involved in the morphology shift of the model diatom species Phaeodactylum tricornutum during surface colonization. We also provide a workflow for characterizing biofouling transformants. By using this protocol, gene targets such as GPCR signaling genes could be identified and manipulated to turn off diatom biofouling. For complete information on the generation and use of this protocol, please refer to Fu et al. (2020).

Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation

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.

Evolution and enrichment of CYP5035 in Polyporales: functionality of an understudied P450 family

Abstract

Bioprospecting for innovative basidiomycete cytochrome P450 enzymes (P450s) is highly desirable due to the fungi’s enormous enzymatic repertoire and outstanding ability to degrade lignin and detoxify various xenobiotics. While fungal metagenomics is progressing rapidly, the biocatalytic potential of the majority of these annotated P450 sequences usually remains concealed, although functional profiling identified several P450 families with versatile substrate scopes towards various natural products. Functional knowledge about the CYP5035 family, for example, is largely insufficient. In this study, the families of the putative P450 sequences of the four white-rot fungi Polyporus arcularius, Polyporus brumalis, Polyporus squamosus and Lentinus tigrinus were assigned, and the CYPomes revealed an unusual enrichment of CYP5035, CYP5136 and CYP5150. By computational analysis of the phylogeny of the former two P450 families, the evolution of their enrichment could be traced back to the Ganoderma macrofungus, indicating their evolutionary benefit. In order to address the knowledge gap on CYP5035 functionality, a representative subgroup of this P450 family of P. arcularius was expressed and screened against a test set of substrates. Thereby, the multifunctional enzyme CYP5035S7 converting several plant natural product classes was discovered. Aligning CYP5035S7 to 102,000 putative P450 sequences of 36 fungal species from Joint Genome Institute-provided genomes located hundreds of further CYP5035 family members, which subfamilies were classified if possible. Exemplified by these specific enzyme analyses, this study gives valuable hints for future bioprospecting of such xenobiotic-detoxifying P450s and for the identification of their biocatalytic potential.

Graphical abstract

Key points

• The P450 families CYP5035 and CYP5136 are unusually enriched in P. arcularius.

• Functional screening shows CYP5035 assisting in the fungal detoxification mechanism.

• Some Polyporales encompass an unusually large repertoire of detoxification P450s.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11444-2.

Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution

Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e-4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance.

Plant cytochrome P450 plasticity and evolution

The superfamily of cytochrome P450 (CYP) enzymes plays key roles in plant evolution and metabolic diversification. This review provides a status on the CYP landscape within green algae and land plants. The 11 conserved CYP clans known from vascular plants are all present in green algae and several green algae-specific clans are recognized. Clan 71, 72, and 85 remain the largest CYP clans and include many taxa-specific CYP (sub)families reflecting emergence of linage-specific pathways. Molecular features and dynamics of CYP plasticity and evolution are discussed and exemplified by selected biosynthetic pathways. High substrate promiscuity is commonly observed for CYPs from large families, favoring retention of gene duplicates and neofunctionalization, thus seeding acquisition of new functions. Elucidation of biosynthetic pathways producing metabolites with sporadic distribution across plant phylogeny reveals multiple examples of convergent evolution where CYPs have been independently recruited from the same or different CYP families, to adapt to similar environmental challenges or ecological niches. Sometimes only a single or a few mutations are required for functional interconversion. A compilation of functionally characterized plant CYPs is provided online through the Plant P450 Database (erda.dk/public/vgrid/PlantP450/).

The Impact of Direct-Acting Antiviral Therapy on End-Stage Liver Disease Among Individuals with Chronic Hepatitis C and Substance Use Disorders

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.

Differential Cost-Sharing Undermines Treatment Adherence to Combination Therapy: Evidence from Diabetes Treatment

INTRODUCTION

The objective of this study was to measure the influence of differences in out-of-pocket (OOP) costs for type 2 diabetes (T2D) medications on within-patient adherence behavior towards combination drug therapy regimens.

METHODS

This was an observational, retrospective, paired sample study in patients with T2D using longitudinal pharmacy data from the 2009-2014 Medical Expenditure Panel Survey (MEPS) augmented with socio-demographic factors. We took a within-patient approach to minimize confounding effects by including patients who maintained the same number of diabetes drug classes over 2 years of MEPS. For each patient, we selected the most and least costly drug classes in the second year and examined their corresponding adherence behavior measured by medication possession ratio. The primary hypothesis tested the significance of the correlation between magnitude of the OOP cost difference and behavioral response in adherence.

RESULTS

Analysis included 1189 patients representing over 4.2 million US residents with T2D. A significant negative correlation (p < 0.001) was observed between the differences of OOP costs and adherence to the most and least costly medications compared within patients. Reduction in adherence to the most costly medication was generally observed when the difference in OOP costs was greater than $33/month. A greater variability in adherence was observed when the cost difference exceeded $2.39/month as compared to other cost difference ranges (p < 0.001), indicative of choices being made.

CONCLUSIONS

As OOP costs increased, adherence variability increased initially until a cost threshold, beyond which the adherence to the more costly medication decreased. In addition to OOP cost, adherence was also influenced by type of medication and self-perception of health. Given the complex correlation between OOP costs and adherence to medication, we suggest a careful approach to cost-sharing in the current insurance drug design and relevant insurance policies.

Predictors of 30-day readmission and hospitalization costs of patients with hepatic encephalopathy in the US from 2010 to 2014

Background: 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.Research design and methods: 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.Results: 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.Conclusions: 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.

Willingness to participate in research among black patients with liver disease: A national cross-sectional study

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.