The role of horizontal gene transfer in the evolution of the oomycetes

This is the final version of the article. Available from Public Library of Science via the DOI in this record.Horizontal gene transfer (HGT) or lateral gene transfer (LGT) involves the transmission of genetic material between distinct evolutionary lineages and can be an important source of biological innovation. For instance, the acquisition of foreign genes can allow recipient organisms to adapt to new lifestyles or to exploit a novel ecological niche, such as a host environment. HGT has long been recognised as an important factor contributing to the evolution of prokaryotic lineages especially in connection to the evolution of pathogencity [1,2]. However, it is becoming increasingly apparent that HGT has also played a role in the evolution of pathogenic traits in eukaryotes [3,4]. Here, we consider how HGT has contributed to genome evolution in the oomycetes

The Second Triennial Systematic Literature Review of European Nursing Research: Impact on Patient Outcomes and Implications for Evidence-Based Practice

This is the final version. Available from Wiley via the DOI in this record. Background: European research in nursing has been criticized as overwhelmingly descriptive, wasteful and with little relevance to clinical practice. This second triennial review follows our previous review of articles published in 2010, to determine whether the situation has changed. Objective: To identify, appraise, and synthesize reports of European nursing research published during 2013 in the top 20 nursing research journals. Methods: Systematic review with descriptive results synthesis. Results: We identified 2,220 reports, of which 254, from 19 European countries, were eligible for analysis; 215 (84.7%) were primary research, 36 (14.2%) secondary research, and three (1.2%) mixed primary and secondary. Forty-eight (18.9%) of studies were experimental: 24 (9.4%) randomized controlled trials, 11 (4.3%) experiments without randomization, and 13 (5.1%) experiments without control group. A total of 106 (41.7%) articles were observational: 85 (33.5%) qualitative research. The majority (158; 62.2%) were from outpatient and secondary care hospital settings. One hundred and sixty-five (65.0%) articles reported nursing intervention studies: 77 (30.3%) independent interventions, 77 (30.3%) interdependent, and 11 (4.3%) dependent. This represents a slight increase in experimental studies compared with our previous review (18.9% vs. 11.7%). The quality of reporting remained very poor. Linking Evidence to Action: European research in nursing remains overwhelmingly descriptive. We call on nursing researchers globally to raise the level of evidence and, therefore, the quality of care and patient outcomes. We urge them to replicate our study in their regions, diagnose reasons for the lack of appropriate research, identify solutions, and implement a deliberate, targeted, and systematic global effort to increase the number of experimental, high quality, and relevant studies into nursing interventions. We also call on journal editors to mandate an improvement in the standards of research reporting in nursing journals

Ancestral function and diversification of a horizontally acquired oomycete carboxylic acid transporter

This is the author accepted manuscript. The final version is available from OUP via the DOI in this recordHorizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonise new environments. However, few studies have characterised the functions of HGT genes experimentally or examined post-acquisition functional divergence. Here we report the use of ancestral sequence reconstruction and heterologous expression in Saccharomyces cerevisiae to examine the evolutionary history of an oomycete transporter gene family that was horizontally acquired from fungi. We demonstrate that the inferred ancestral oomycete HGT transporter proteins and their extant descendants are predominantly localised to the plasma membrane when expressed in yeast, and that they transport dicarboxylic acids which are intermediates of the tricarboxylic acid cycle. The substrate specificity profile of the most ancestral protein has largely been retained throughout the radiation of oomycetes, including in both plant and animal pathogens and in a free-living saprotroph, indicating that the ancestral HGT transporter function has been maintained by selection across a range of different lifestyles. No evidence of neofunctionalization in terms of substrate specificity was detected for different HGT transporter paralogues which have different patterns of temporal expression. However, a striking expansion of substrate range was observed for one plant pathogenic oomycete, with a HGT derived paralogue from Pythium aphanidermatum encoding a protein that enables tricarboxylic acid uptake in addition to dicarboxylic acid uptake. This demonstrates that HGT acquisitions can provide functional additions to the recipient proteome as well as the foundation material for the evolution of new protein functions.This work was supported by a Philip Leverhulme Award to T. A. R. We acknowledge related project funding from the Gordon and Betty Moore Foundation (GBMF5514). T.A.R. is supported by a Royal Society University Research Fellowshi

Nematopsis temporariae (Gregarinasina, Apicomplexa, Alveolata) intracellular infectious agent of tadpole livers

Amphibians are in decline as a result of habitat destruction, climate change and infectious diseases. Tadpoles are thought susceptible to infections because they are dependent on only an innate immune system (e.g. macrophages). This is because the frog adaptive immune system does not function until later stages of the life cycle. In 1920, Nöller described a putative infectious agent of tadpoles named Nematopsis temporariae, which he putatively assigned to gregarine protists (Apicomplexa). Here, we identify a gregarine infection of tadpoles using both microscopy and ribosomal DNA sequencing of three different frog species (Rana temporaria, R. dalmatina, and Hyla arborea). We show that this protist lineage belongs to the subclass Gregarinasina Dufour 1828 and is regularly present in macrophages located in liver sinusoids of tadpoles, confirming the only known case of a gregarine infection of a vertebrate. This article is protected by copyright. All rights reserved.Marie Curie Intra-European and EMBO Long-Term Fellowships . Grant Number: FP7-PEOPLE-2011-IEF-299815-PARAFROGS and ATL-1069-2011. Czech Science Foundation . Grant Number: GBP505/12/G112-ECI

The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer

This is the final version. Available on open access from Oxford University Press via the DOI in this recordSaprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the "secretome" and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here, we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle.University of Rhode Island College of the Environment and Life SciencesU.S. Department of AgricultureNational Institutes of Health (NIH)National Science FoundationDivision of Biology and Medicine, Brown Universit

Complex patterns of gene fission in the eukaryotic folate biosynthesis pathway

This is the final version. Available on open access from Oxford University Press via the DOI in this recordShared derived genomic characters can be useful for polarizing phylogenetic relationships, for example, gene fusions have been used to identify deep-branching relationships in the eukaryotes. Here, we report the evolutionary analysis of a three-gene fusion of folB, folK, and folP, which encode enzymes that catalyze consecutive steps in de novo folate biosynthesis. The folK-folP fusion was found across the eukaryotes and a sparse collection of prokaryotes. This suggests an ancient derivation with a number of gene losses in the eukaryotes potentially as a consequence of adaptation to heterotrophic lifestyles. In contrast, the folB-folK-folP gene is specific to a mosaic collection of Amorphea taxa (a group encompassing: Amoebozoa, Apusomonadida, Breviatea, and Opisthokonta).Next, we investigated the stability of this character.We identified numerous gene losses and a total of nine gene fission events, either by break up of an open reading frame (four events identified) or loss of a component domain (five events identified). This indicates that this three gene fusion is highly labile. These data are consistent with a growing body of data indicating gene fission events occur at high relative rates. Accounting for these sources of homoplasy, our data suggest that the folB-folK-folP gene fusion was present in the last common an castor of Amoebozoa and Opisthokonta but absent inthe Metazoa including the human genome. Comparative genomic data of these genes provides an important resource for designing therapeutic strategies targeting the de novo folate biosynthesis pathway of a variety of eukaryotic pathogens such as Acanthamoeba castellanii.Society of General MicrobiologyTula Foundation (The Centre for Comparative Genomics and Evolutionary Bioinformatics at Dalhousie University)Gordon and Betty Moore FoundationLeverhulme TrustRoyal SocietyNatural Environment Research Council (NERC)Biotechnology and Biological Sciences Research Council (BBSRC

The effectiveness and cost-effectiveness of telephone triage of patients requesting same day consultations in general practice: study protocol for a cluster randomised controlled trial comparing nurse-led and GP-led management systems (ESTEEM)

notes: PMCID: PMC3574027This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Recent years have seen an increase in primary care workload, especially following the introduction of a new General Medical Services contract in 2004. Telephone triage and telephone consultation with patients seeking health care represent initiatives aimed at improving access to care. Some evidence suggests that such approaches may be feasible but conclusions regarding GP workload, cost, and patients' experience of care, safety, and health status are equivocal. The ESTEEM trial aims to assess the clinical- and cost-effectiveness of nurse-led computer-supported telephone triage and GP-led telephone triage, compared to usual care, for patients requesting same-day consultations in general practice.UK National Institute of Health Research Health Technology Assessment programmeDepartment of Healt

Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments

This is the final published PDF. Available from BMC via the DOI in this record.Background Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity ‘tag’ sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations. Results We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity suggesting this diversity encompasses a range of biologically and ecologically distinct organisms. Conclusions These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally ‘active’ and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the ‘seed bank’ microbial community.Marie Curie Intra-European Fellowship grantEMBO Long-Term fellowshipGordon and Betty Moore Foundatio

Duration of untreated eating disorder and relationship to outcomes: A systematic review of the literature

Objective: This systematic review assesses the average duration of untreated eating disorder (DUED) in help‐seeking populations at the time of first eating disorder (ED) treatment and investigates the relationship between DUED and symptom severity/clinical outcomes. / Method: PRISMA guidelines were followed throughout. Selected studies provided information on either: (i) length of DUED, (ii) components of DUED, (iii) cross‐sectional associations between DUED and symptom severity, (iv) associations between DUED and clinical outcomes, or (v) experimental manipulation of DUED. Study quality was assessed. / Results: Fourteen studies from seven countries were included. Across studies, average DUED weighted by sample size was 29.9 months for anorexia nervosa, 53.0 months for bulimia nervosa and 67.4 months for binge eating disorder. A younger age at time of first treatment was indicative of shorter DUED. Retrospective studies suggest that a shorter DUED may be related to a greater likelihood of remission. Manipulation of DUED by shortening service‐related delays may improve clinical outcomes. / Conclusions: Data on length of DUED provide a benchmark for early intervention in EDs. Preliminary evidence suggests DUED may be a modifiable factor influencing outcomes in EDs. To accurately determine the role of DUED, definition and measurement must be uniformly operationalised

A Candidate Sub-Parsec Supermassive Binary Black Hole System

We identify SDSS J153636.22+044127.0, a QSO discovered in the Sloan Digital Sky Survey, as a promising candidate for a binary black hole system. This QSO has two broad-line emission systems separated by 3500 km/sec. The redder system at z=0.3889 also has a typical set of narrow forbidden lines. The bluer system (z=0.3727) shows only broad Balmer lines and UV Fe II emission, making it highly unusual in its lack of narrow lines. A third system, which includes only unresolved absorption lines, is seen at a redshift, z=0.3878, intermediate between the two emission-line systems. While the observational signatures of binary nuclear black holes remain unclear, J1536+0441 is unique among all QSOs known in having two broad-line regions, indicative of two separate black holes presently accreting gas. The interpretation of this as a bound binary system of two black holes having masses of 10^8.9 and 10^7.3 solar masses, yields a separation of ~ 0.1 parsec and an orbital period of ~100 years. The separation implies that the two black holes are orbiting within a single narrow-line region, consistent with the characteristics of the spectrum. This object was identified as an extreme outlier of a Karhunen-Loeve Transform of 17,500 z < 0.7 QSO spectra from the SDSS. The probability of the spectrum resulting from a chance superposition of two QSOs with similar redshifts is estimated at 2X10^-7, leading to the expectation of 0.003 such objects in the sample studied; however, even in this case, the spectrum of the lower redshift QSO remains highly unusual.Comment: 8 pages, 2 figures, Nature in pres