Lepidopteran Granivory Reduces Seed Counts in a Rare Species of Riparian Scour Prairies

In Pennsylvania Baptisia australis var. australis is found along only four waterways: the Allegheny River, Youghiogheny River, Clarion River, and Red Bank Creek. Because of its limited distribution and small number of extant populations, the species is considered state-threatened in Pennsylvania. In addition, the riparian prairie habitat that Pennsylvania Baptisia australis var. australis is restricted to is also in decline and considered vulnerable. Because of these conservation concerns, insights into the natural history of the taxon in the state is valuable and will inform conservation efforts. Field surveys and fruit collections along the Allegheny River and herbarium collections were used to investigate and document granivory in Pennsylvania Baptisia australis var. australis, a phenomenon recorded in other parts of the species\u27 range, but not previously reported on in Pennsylvania. Using a model of best fit, the number of seeds found in fruit was found to be significantly impacted by the presence of granivores. We also report that visual surveys of fruits in the field are found to be accurate assessments of the presence and potential impact of granivores. In turn, our results will inform the conservation and management of Baptisia australis var. australis populations in Pennsylvania and highlight the importance of field surveys in protecting threatened taxa

Temperate Eurasian Origins of Hawaiian Chenopodium (Amaranthaceae) plus description of a new species endemic to Moloka‘i

Chenopodium taxa of Hawai‘i are tetraploids distinguished from other members of the circumglobally distributed genus by minute morphological characters. Because of these reasons, the geographic origin of Hawaiian Chenopodium has remained unclear. Across the Hawaiian Archipelago, Chenopodium taxa are morphologically variable and grow in highly disparate xeric habitats, especially in terms of precipitation, temperature, wind, salt spray, and solar irradiation. Habitats include dry subalpine shrublands, sandy beach strand of atolls in the Northwest Hawaiian Islands, dry forests, and precipitously tall sea cliffs of northwestern Moloka‘i. From the Moloka‘i sea cliffs, which are battered by high energy winds, salt spray, and strong seasonal precipitation, we describe C. oahuense subspecies ilioensis as segregated from the widespread Hawaiian C. oahuense s.l. Morphometric analyses distinguish C. oahuense ssp. ilioensis through its strongly prostrate to scandent habit, thick succulent leaves, smaller average leaf sizes, limited leaf margin lobing, and smaller seeds. Phylogenetic analyses using two DNA regions (the plastid gene rpl32-trnL and nuclear ITS1-5.85 rDNA-ITS2) of newly sequenced C. oahuense s.l. and C. oahuense ssp. ilioensis individuals plus outgroup taxa support monophyly of Hawaiian Chenopodium and reveal a geographic origin of temperate Eurasia. Two equivocal hypothetical scenarios are discussed regarding the likely sequence of events leading to the arrival of Chenopodium in Hawaiian Islands followed by possible in situ speciation of the Moloka‘i endemic C. oahuense ssp. ilioensis

Integrated pest management in the academic small greenhouse setting: A case study using Solanum spp. (Solanaceae).

Premise Botanical faculty and staff at academic institutions are often tasked with establishing and/or caring for plant collections held in small greenhouse facilities. Once plants are in place, an especially acute challenge is managing plant pest/pathogen populations. Integrated pest management (IPM) approaches are an excellent option, but few examples exist in the literature of successful programs that have been developed in academic small greenhouse settings. Methods and Results Over several years, we developed an IPM program for two small research greenhouses on the campus of a primarily undergraduate institution where hundreds of plants have been grown for studies in the genus Solanum. We here present a synopsis of the cultural, mechanical, physical, and biological controls used as part of our successful IPM strategy—including details on the efficacy of multiple predatory insects—with the hope of providing a model for sustainable pest management in the higher education environment. Conclusions IPM can be an effective strategy for maintaining healthy plant populations in small research greenhouses, but it requires a consistent investment of time and funding. A well‐cared‐for plant collection might help support numerous positive outcomes, including advances in faculty scholarship and opportunities for student learning and/or training

Phylogeny of the Australian Solanum dioicum group using seven nuclear genes: Testing Symon’s fruit and seed dispersal hypotheses.

The dioecious and andromonoecious Solanum taxa (the “S. dioicum group”) of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed dispersal (strongly linked to calyx accrescence) is far more common among Australian Solanum than previously thought and support the hypothesis that the combination of large fleshy fruits and endozoochorous dispersal represents a reversal in this study group. The general lack of direct evidence related to biotic dispersal (epizoochorous or endozoochorous) may be a function of declines and/or extinctions of vertebrate dispersers. Because of this, some taxa might now rely on secondary dispersal mechanisms (e.g. shakers, tumbleweeds, rafting) as a means to maintain current populations and establish new ones

Reproducible protocols for metagenomic analysis of human faecal phageomes

peer-reviewedAll sequence data used in the analyses were deposited in the Sequence read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under BioProject PRJNA407341. Sample IDs, meta data and corresponding accession numbers are summarised in Additional file 2: Table S2. All raw count tables, 16S taxonomic assignments, BLAST top hits for viral contigs and R code used for the analysis are available at (https://figshare.com/s/71163558b4f78e3e7ed6).Background Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing. Results Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples. Conclusions The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results

Phylogenomic Discordance Suggests Polytomies Along the Backbone of the Large Genus Solanum

Premise of the study Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. Methods A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). Key results While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. Conclusions We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages

The independent contribution of <i>Pseudomonas aeruginosa</i> infection to long-term clinical outcomes in bronchiectasis

Pseudomonas aeruginosa is responsible for chronic infection in many bronchiectasis patients but it is not known whether it is associated with worse clinical outcomes independent of the underlying severity of disease. This study analysed data from 2596 bronchiectasis patients included from 10 different bronchiectasis clinical centres across Europe and Israel, with a 5-year follow-up period. Prevalence of P. aeruginosa chronic infection and its independent impact on exacerbations, hospitalisations, quality of life and mortality was assessed. The prevalence of P. aeruginosa chronic infection was 15.0% (n=389). P. aeruginosa was associated with a higher mortality in a univariate analysis (hazard ratio (HR) 2.02; 95% (confidence interval) CI 1.53-2.66; p&lt;0.0001) but an independent impact on mortality was not found in a multivariate analysis (HR 0.98; 95% CI 0.70-1.36; p=0.89). P. aeruginosa was independently associated with increased mortality only in patients with frequent exacerbations (two or more per year) (HR 2.03; 95% CI 1.36-3.03; p=0.001). An independent association with worse quality of life of 7.46 points (95% CI 2.93-12.00; p=0.001) was found in a multivariable linear regression. P. aeruginosa was therefore found to be independently associated with exacerbation frequency, hospital admissions and worse quality of life. Mortality was increased in patients with P. aeruginosa particularly in the presence of frequent exacerbations

Dose-associated changes in safety and efficacy parameters observed in a 24-week maintenance trial of olanzapine long-acting injection in patients with schizophrenia

<p>Abstract</p> <p>Background</p> <p>In a recently published 24-week maintenance study of olanzapine long-acting injection (LAI) in schizophrenia (Kane et al., 2010), apparent dose-associated changes were noted in both efficacy and safety parameters. To help clinicians balance safety and efficacy when choosing a dose of olanzapine LAI, we further studied these changes.</p> <p>Methods</p> <p>Outpatients with schizophrenia who had maintained stability on open-label oral olanzapine for 4 to 8 weeks were randomly assigned to "low" (150 mg/2 weeks; N = 140), "medium" (405 mg/4 weeks; N = 318), or "high" (300 mg/2 weeks; N = 141) dosages of olanzapine LAI for 24 weeks. Potential relationships between dose and several safety or efficacy measures were examined via regression analysis, the Jonckheere-Terpstra test (continuous data), or the Cochran-Armitage test (categorical data).</p> <p>Results</p> <p>Safety parameters statistically significantly related to dose were mean weight change (low: +0.67 [SD = 4.38], medium: +0.89 [SD = 3.87], high: +1.70 [SD = 4.14] kg, p = .024; effect size [ES] = 0.264 high vs. low dose), mean change in prolactin (low: -5.61 [SD = 12.49], medium: -2.76 [SD = 19.02]), high: +3.58 [SD = 33.78] μg/L, p = .001; ES = 0.410 high vs. low dose), fasting triglycerides change from normal at baseline to high (low: 3.2%, medium: 6.0%, high: 18.9%, p = .001; NNT = 7 high vs. low dose) and fasting high-density lipoprotein cholesterol change from normal at baseline to low (low: 13.8%, medium: 19.6%, high: 30.7%, p = .019; NNT = 6 high vs. low dose). Efficacy measures significantly related to dose included Positive and Negative Syndrome Scale total score mean change (low: +2.66 [SD = 14.95], medium: -0.09 [SD = 13.47], high: -2.19 [SD = 13.11], p <.01; ES = 0.356 high vs. low dose), relapse rate (low: 16%, medium: 10%, high: 5%, p = .003; NNT = 9 high vs. low dose), all-cause discontinuation rate (low: 36%, medium: 30%, high: 24%, p = .037; NNT = 9 high vs. low dose), and rate of discontinuation due to efficacy-related reasons (low: 20%, medium: 14%, high: 6%, p <.001). Time to all-cause discontinuation (p = .035) and time to relapse (p = .005) were also significantly related to dose.</p> <p>Conclusions</p> <p>Analyses of several safety and efficacy parameters revealed significant associations with dose of olanzapine LAI, with the highest dose generally showing greater efficacy as well as greater adverse changes in metabolic safety measures. When considering olanzapine LAI, as with all antipsychotics, it is important to carefully consider the potential benefits and risks for an individual patient.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT00088491">NCT00088491</a></p

The Problematization of Sexuality among Women Living with HIV and a New Feminist Approach for Understanding and Enhancing Women’s Sexual Lives

In the context of HIV, women’s sexual rights and sexual autonomy are important but frequently overlooked and violated. Guided by community voices, feminist theories, and qualitative empirical research, we reviewed two decades of global quantitative research on sexuality among women living with HIV. In the 32 studies we found, conducted in 25 countries and composed mostly of cis-gender heterosexual women, sexuality was narrowly constructed as sexual behaviours involving risk (namely, penetration) and physiological dysfunctions relating to HIV illness, with far less attention given to the fullness of sexual lives in context, including more&nbsp;positive and rewarding experiences such as satisfaction and pleasure. Findings suggest that women experience declines in sexual activity, function, satisfaction, and pleasure following HIV diagnosis, at least for some period. The extent of such declines, however, is varied, with numerous contextual forces shaping women’s sexual well-being. Clinical markers of HIV (e.g., viral load, CD4 cell count) poorly predicted sexual outcomes, interrupting widely held assumptions about sexuality for women with HIV. Instead, the effects of HIV-related stigma intersecting with inequities related to trauma, violence, intimate relations, substance use, poverty, aging, and other social and cultural conditions primarily influenced the ways in which women experienced and enacted their sexuality. However, studies framed through a medical lens tended to pathologize outcomes as individual “problems,” whereas others driven by a public health agenda remained primarily preoccupied with protecting the public from HIV. In light of these findings, we present a new feminist approach for research, policy, and practice toward understanding and enhancing women’s sexual lives—one that affirms sexual diversity; engages deeply with society, politics, and history; and is grounded in women’s sexual rights