Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification.

PREMISE: Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear. METHODS: Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations. RESULTS: The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology. CONCLUSIONS: We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.

A target enrichment probe set for resolving the flagellate land plant tree of life.

PREMISE: New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. METHODS: We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages. RESULTS: Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. CONCLUSIONS: A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

The bacterial communities of Alaskan mosses and their contributions to N2-fixation.

BACKGROUND: Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N2-fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N2-fixation rates via 15N2 isotopic enrichment and identified potential N2-fixing bacteria using available literature and genomic information. RESULTS: Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N2-fixing bacteria specific to some moss hosts, including potential N2-fixing bacteria outside well-studied cyanobacterial clades. CONCLUSIONS: The strong effect of host identity on moss-associated bacterial communities demonstrates mosses' utility for understanding plant-microbe interactions in non-leguminous systems. Our work also highlights the likely importance of novel bacterial taxa to N2-fixation in high-latitude ecosystems. Video Abstract.

Exposure to di(2-ethylhexyl) phthalate and diisononyl phthalate during adulthood disrupts hormones and ovarian folliculogenesis throughout the prime reproductive life of the mouse.

Di(2-ethylhexyl) phthalate (DEHP) is a phthalate commonly used for its plasticizing capabilities. Because of the wide production and use of DEHP, humans are exposed to DEHP on a daily basis. Diisononyl phthalate (DiNP) is often used as a DEHP replacement chemical, and because of the increased use of DiNP, humans are increasingly exposed to DiNP over time. Of concern is that DEHP and DiNP both exhibit endocrine disrupting capabilities, and little is known about how short-term exposure to either of these phthalates affects aspects of female reproduction. Thus, this study tested the hypothesis that short-term exposure to DEHP or DiNP during adulthood has long-lasting consequences on ovarian follicles and hormones in female mice. Female CD-1 mice aged 39-40 days were orally dosed with either vehicle control (corn oil), DEHP (20 µg/kg/day-200 mg/kg/day), or DiNP (20 µg/kg/day-200 mg/kg/day) for 10 days. Ovarian follicle populations, estradiol, testosterone, progesterone, follicle stimulating hormone (FSH), and inhibin B were analyzed at time points immediately post-dosing and 3, 6, and 9 months post-dosing. The results indicate that 10 days of exposure to DEHP and DiNP changed the distribution of ovarian follicle populations and sex steroid hormones at multiple time points, including the last time point, 9 months post-dosing. Further, FSH was increased at multiple doses up to 6 months post-dosing. Inhibin B was not affected by treatment. These data show that short-term exposure to either DEHP or DiNP has long-term consequences that persist long after cessation of exposure.

Late-life consequences of short-term exposure to di(2-ethylhexyl) phthalate and diisononyl phthalate during adulthood in female mice.

Di(2-ethylhexyl) phthalate (DEHP) is a known endocrine disruptor and diisononyl phthalate (DiNP) is a common DEHP replacement chemical. However, little is known about late-life consequences due to DEHP or DiNP exposure during adulthood. Thus, this study tested the hypothesis that adult exposure to DEHP or DiNP affects female reproductive parameters during late-life in female mice. Female CD-1 mice (age 39-40 days) were dosed with either vehicle control, DEHP (20 µg/kg/day-200 mg/kg/day), or DiNP (20 µg/kg/day-200 mg/kg/day) for 10 days and breeding trials were conducted at 12 and 15 months post-dosing. Further, ovaries and sera were collected at 12, 15, and 18 months post-dosing. DEHP and DiNP disrupted estrous cyclicity, increased pregnancy loss, decreased fertility, altered the sex ratio of pups, altered ovarian follicle populations, and disrupted hormone levels. Collectively, these data show that short-term exposure to DEHP or DiNP during adulthood has long-term consequences in late-life.

Novel bacterial lineages associated with boreal moss species.

Mosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbour diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local site conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with seven boreal moss species collected near Fairbanks, AK, USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbour diverse lineages of potential N2 -fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.

Infraspecific variation within and across complete organellar genomes and nuclear ribosomal repeats in a moss.

Bryophytes (mosses, liverworts, and hornworts) are diverse and ecologically and evolutionarily significant yet genome scale data sets and analyses remain extremely sparse relative to other groups of plants, and are completely lacking at the infraspecific level. By sequencing the complete organellar genomes and nuclear ribosomal repeat from seven patches of a South American sub-Antarctic neo-endemic non-model moss, we present the first characterization of infraspecific polymorphism within and across the three genomic compartments for a bryophyte. Diversity within patches is accounted for by both intraindividual and interindividual variation for the nuclear ribosomal repeat and plastid genome, respectively. This represents the most extensive infraspecific genomic dataset generated for an early land plant lineage thus far and provides insight into relative rates of substitution between organellar genomes, including high rates of nonsynonymous to synonymous substitutions.

Budget impact analysis of everolimus for the treatment of hormone receptor positive, human epidermal growth factor receptor-2 negative (HER2-) advanced breast cancer in Kazakhstan.

OBJECTIVE: The aim of this study was to determine the budget impact of everolimus (in combination with letrozole/anastrozole) as a second-line treatment for ER+ HER2- negative advanced and metastatic breast cancer in post-menopausal women. RESEARCH DESIGN AND METHODS: A cumulative cohort model was developed to estimate the 5-year costs associated with introducing everolimus to the Kazakh healthcare system. Two alternative market share scenarios were compared: with everolimus and without everolimus. PFS and OS data were taken from the trial and extrapolated. The background costs of the pre-progressed and post-progressed health states, drug costs and costs associated with adverse events were included in the model. RESULTS: The 5-year results from the budget impact analysis demonstrate that the introduction of everolimus leads to a 12% increase in drug costs, a 2% reduction in pre-progression health state costs, a 1% increase in post-progression health state costs, and a 2% reduction in adverse event costs. The net result is only a modest increase in total costs; a 2.69% increase of T201 million, from T7.5 billion to T7.7 billion over a period of 5 years. CONCLUSIONS: The analysis estimated that, if everolimus were to be introduced to the Kazakh healthcare market for the treatment of ER+ HER2- advanced breast cancer, there would be minimal impact upon overall healthcare expenditure. An increase in drug acquisitions costs was almost exactly offset by a reduction in other healthcare costs, due to improved management of the disease.

Cost-effectiveness of pazopanib in advanced soft tissue sarcoma in the United kingdom.

In the phase III PALETTE trial, pazopanib improved progression-free survival (PFS) compared with placebo in patients with advanced/metastatic soft tissue sarcomas (mSTS) who had received prior chemotherapy. We used a multistate model to estimate expected PFS, overall survival (OS), lifetime STS treatment costs, and quality-adjusted life-years (QALYs) for patients receiving pazopanib, placebo, trabectedin, ifosfamide, or gemcitabine plus docetaxel as second-line mSTS therapies. The cost-effectiveness of pazopanib was expressed as the incremental costs per QALY gained. Estimates of PFS/OS, adverse events, and utilities for pazopanib and placebo were from the PALETTE trial. Estimates of relative effectiveness of the other comparators were from an unadjusted indirect comparison versus pazopanib. Costs were from published sources. Pazopanib is estimated to increase QALYs by 0.128 and costs by £7,976 versus placebo; cost per QALY gained with pazopanib versus placebo is estimated to be £62,000. Compared with the other chemotherapies, pazopanib provides similar QALYs at a lower cost. Pazopanib may not be cost-effective versus placebo but may be cost-effective versus the most commonly used active treatments, although this conclusion is uncertain. Given the unmet need for effective treatments for mSTS, pazopanib may be an appropriate alternative to some currently used medications in the United Kingdom.

First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds.

Correlations between transequatorial migratory bird routes and bipolar biogeographic disjunctions in bryophytes suggest that disjunctions between northern and southern high latitude regions may result from bird-mediated dispersal; supporting evidence is, however, exclusively circumstantial. Birds disperse plant units (diaspores) internally via ingestion (endozoochory) or externally by the attachment of diaspores to the body (ectozoochory). Endozoochory is known to be the primary means of bird-mediated dispersal for seeds and invertebrates at local, regional, and continental scales. Data supporting the role of bird-mediated endozoochory or ectozoochory in the long distance dispersal of bryophytes remain sparse, however, despite the large number of bryophytes displaying bipolar disjunctions. To determine if transequatorial migrant shorebirds may play a role in the ectozoochory of bryophyte diaspores, we developed a method for screening feathers of wild birds. We provide the first evidence of microscopic bryophyte diaspores, as well as those from non-bryophyte lineages, embedded in the plumage of long distance transequatorial migrant birds captured in their arctic breeding grounds. The number of diaspores recovered suggests that entire migratory populations may be departing their northern breeding grounds laden with potentially viable plant parts and that they could thereby play significant roles in bipolar range expansions of lineages previously ignored in the migrant bird dispersal literature.

Early intervention in Alzheimer's disease: a health economic study of the effects of diagnostic timing.

BACKGROUND: Intervention and treatment in Alzheimer's disease dementia (AD-dementia) can be cost effective but the majority of patients are not diagnosed in a timely manner. Technology is now available that can enable the earlier detection of cognitive loss associated with incipient dementia, offering the potential for earlier intervention in the UK health care system. This study aimed to determine to what extent the timing of an intervention affects its cost-effectiveness. METHODS: Using published data describing cognitive decline in the years prior to an AD diagnosis, we modelled the effects on healthcare costs and quality-adjusted life years of hypothetical symptomatic and disease-modifying interventions. Early and standard interventions were assumed to have equal clinical effects, but the early intervention could be applied up to eight years prior to standard diagnosis. RESULTS: A symptomatic treatment which immediately improved cognition by one MMSE point and reduced in efficacy over three years, would produce a maximum net benefit when applied at the earliest timepoint considered, i.e. eight years prior to standard diagnosis. In this scenario, the net benefit was reduced by around 17% for every year that intervention was delayed. In contrast, for a disease-modifying intervention which halted cognitive decline for one year, economic benefits would peak when treatment effects were applied two years prior to standard diagnosis. In these models, the maximum net benefit of the disease modifying intervention was fifteen times larger than that of the symptomatic treatment. CONCLUSION: Timeliness of intervention is likely to have an important impact on the cost-effectiveness of both current and future treatments. Healthcare policy should aim to optimise the timing of AD-dementia diagnosis, which is likely to necessitate detecting and treating patients several years prior to current clinical practice.

A United Kingdom-based economic evaluation of ranibizumab for patients with retinal vein occlusion (RVO).

OBJECTIVE: This study compares the cost-effectiveness of intravitreal ranibizumab vs observation and/or laser photocoagulation for treatment of macular edema secondary to retinal vein occlusion in a UK-based model. METHODS: A Markov model was constructed using transition probabilities and frequency of adverse events derived using data from the BRAVO, CRUISE, and HORIZON trials. Outcomes associated with treatments and health states were combined to predict overall health costs and outcomes for cohorts treated with each option. RESULTS: In branch retinal vein occlusion, ranibizumab produced a gain of 0.518 quality-adjusted life years at an incremental cost of £8141, compared with laser photocoagulation. The incremental cost-effectiveness ratio was £15,710 per quality-adjusted life year, and the incremental cost per month free from blindness was £658. In central retinal vein occlusion, ranibizumab produced a gain of 0.539 quality-adjusted life years at an incremental cost of £9216, compared with observation only. The incremental cost-effectiveness ratio was £17,103, and the incremental cost per month free from blindness was £423. CONCLUSIONS: These incremental cost-effectiveness ratios are below the £20,000-30,000 range typically accepted as a threshold for cost-effectiveness. This suggests that ranibizumab may be regarded as a cost-effective therapy for patients with macular edema secondary to retinal vein occlusion, relative to grid laser photocoagulation (for BRVO) and observation (for CRVO). Limitations include sparse data for utilities associated with the severity of visual impairment in the WSE in patients with RVO. A lack of direct comparative evidence between ranibizumab and the dexamethasone intravitreal implant for the treatment of BRVO and CRVO and the infeasibility of an indirect comparison due to significant heterogeneity in trial designs prevented the inclusion of this treatment as a comparator in the Markov model.

High readmission rates are associated with a significant economic burden and poor outcome in patients with grade III/IV acute GvHD.

Graft-versus-host disease (GvHD) is a common complication following haematopoietic stem cell transplant but little is published about the impact of this condition on hospital readmission rates. We report a retrospective analysis of readmission rates and associated costs in 187 consecutive allogeneic transplant patients to assess the impact of GvHD. The overall readmission rate was higher in patients with GvHD (86% (101/118) vs. 59% (41/69), p < 0.001). The readmission rate was higher both in the first 100 d from transplant (p = 0.02) and in the first year following transplant (p < 0.001). 151/455 (33%) of all readmission episodes occurred within 100 d of transplant. The mean number of inpatient days was significantly higher in patients with grade III/IV acute GvHD (101 d) compared with those with grade I/II GvHD (70 d; p = 0.003). The mean cost of readmission was higher in patients with GvHD (£28 860) than in non-GvHD patients (£13 405; p = 0.002) and in patients with grade III/IV GvHD (£40 012) compared with those patients with grade I/II GvHD (£24 560; p = 0.038). Survival was higher in those with grade I/II GvHD (55%) compared to grade III/IV GvHD (14%; p < 0.001). This study shows the high economic burden and poor overall survival associated with grade III/IV GvHD.