Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria

Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.

Bacterial Skin Assemblages of Sympatric Salamanders Are Primarily Shaped by Host Genus

Bacterial assemblages on the skins of amphibians are known to influence pathogen resistance and other important physiological functions in the host. Host-specific factors and the environment play significant roles in structuring skin assemblages. This study used high-throughput 16S rRNA sequencing and multivariate analyses to examine differences in skin-bacterial assemblages from 246 salamanders belonging to three genera in the lungless family Plethodontidae along multiple spatial gradients. Composition and α- and β-diversity of bacterial assemblages were defined, indicator species were identified for each host group, and the relative influences of host- versus environment-specific ecological factors were evaluated. At the broadest spatial scale, host genus, host species, and sampling site were predictive of skin assemblage structure, but host genus and species were more influential after controlling for the marginal effects of site, as well as nestedness of site. Furthermore, assemblage similarity within each host genus did not change with increasing geographic distance. At the smallest spatial scale, site-specific climate analyses revealed different relationships to climatic variables for each of the three genera, and these relationships were determined by host ecomode. Variation in bacterial assemblages of terrestrial hosts correlated with landscape-level climatic variability, and this pattern decayed with increasing water dependence of the host. Results from this study highlight host-specific considerations for researchers studying wildlife diseases in co-occurring, yet ecologically divergent, species.

Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen

Understanding how host-associated microbial assemblages respond to pathogen invasion has implications for host health. Until recently, most investigations have focused on understanding the taxonomic composition of these assemblages. However, recent studies have suggested that microbial assemblage taxonomic composition is decoupled from its function, with assemblages being taxonomically varied but functionally constrained. The objective of this investigation was to understand how the Tri-colored bat, Perimyotis subflavus cutaneous microbial assemblage responds to fungal pathogen invasion within a functional context. We hypothesized that at a broad scale (e.g., KEGG pathways), there will be no difference in the functional assemblages between the white nose pathogen, Pseudogymnoascus destructans, positive and negative bats; and this pattern will be driven by the functional redundancy of bacterial taxa. At finer scales (e.g., gene models), we postulate differences in function attributed to interactions between bacteria and P. destructans, resulting in the production of antifungal metabolites. To test this, we used a combination of shotgun metagenomic and amplicon sequencing to characterize the bat cutaneous microbial assemblage in the presence/absence of P. destructans. Results showed that while there was a shift in taxonomic assemblage composition between P. destructans positive and negative bats, there was little overall difference in microbial function. Functional redundancy across bacterial taxa was clear at a broad-scale; however, both redundancy and variation in bacterial capability related to defense against pathogens was evident at finer scales. While functionality of the microbial assemblage was largely conserved in relation to P. destructans, the roles of particular functional pathways in resistance to fungal pathogens require further attention.

Testing the febrile response of snakes inoculated with Ophidiomyces ophidiicola, the causative agent of snake fungal disease

Snake Fungal Disease (SFD) negatively impacts wild snake populations in the eastern United States and Europe. Ophidiomyces ophidiicola causes SFD and manifests clinically by the formation of heterophilic granulomas around the mouth and eyes, weight loss, impaired vision, and sometimes death. Field observations have documented early seasonal basking behaviors in severely infected snakes, potentially suggesting induction of a behavioral febrile response to combat the mycosis. This study tested the hypothesis that snakes inoculated with Ophidiomyces ophidiicola would seek elevated basking temperatures to control body temperature and behaviorally induce a febrile response. Eastern ribbon snakes (Thamnophis saurita, n = 29) were experimentally or sham inoculated with O. ophidiicola. Seven days after inoculation, snakes were tested on a thermal gradient and the internal body temperature and substrate temperature of each snake was recorded over time. Quantitative PCR was used when snakes arrived, during pre-inoculation, and post-inoculation to test snakes for the presence of O. ophidiicola. Some snakes arrived with O. ophidiicola and were subsequently inoculated, allowing for an assessment of secondary exposure effects. Snake thermoregulatory behavior was compared between 1) O. ophidiicola inoculated vs. sham inoculated treatments, 2) infected vs. disease negative groups, and 3) disease naïve vs. pre-exposed immune response categories. Neither internal nor substrate temperatures differed among initially prescribed, and qPCR recovered disease states, although infected snakes tended to reach a preferred body temperature faster than disease negative snakes. Snakes experiencing their first exposure (disease naïve) sought higher substrate temperatures than snakes experiencing their second exposure (pre-exposed). Here, we recover no evidence for behaviorally induced fever in snakes with SFD but do elucidate a febrile immune response associated with secondary exposure.

Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales

Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.

The cutaneous microbiota of bats has in vitro antifungal activity against the white nose pathogen

Since its introduction into the USA, Pseudogymnoascus destructans (Pd), the fungal pathogen of white-nose syndrome, has killed millions of bats. Recently, bacteria capable of inhibiting the growth of Pd have been identified within bat microbial assemblages, leading to increased interest in elucidating bacterial assemblage-pathogen interactions. Our objectives were to determine if bat cutaneous bacteria have antifungal activity against Pd, and correlate differences in the bat cutaneous microbiota with the presence/absence of Pd. We hypothesized that the cutaneous microbiota of bats is enriched with antifungal bacteria, and that the skin assemblage will correlate with Pd status. To test this, we sampled bat microbiota, adjacent roost surfaces and soil from Pd positive caves to infer possible overlap of antifungal taxa, we tested these bacteria for bioactivity in vitro, and lastly compared bacterial assemblages using both amplicon and shotgun high-throughput DNA sequencing. Results suggest that the presence of Pd has an inconsistent influence on the bat cutaneous microbial assemblage across sites. Operational taxonomic units (OTUs) that corresponded with cultured antifungal bacteria were present within all sample types but were significantly more abundant on bat skin relative to the environment. Additionally, the microbial assemblage of Pd negative bats was found to have more OTUs that corresponded to antifungal taxa than positive bats, suggesting an interaction between the fungal pathogen and cutaneous microbial assemblage.

Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity

A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.

Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss)

BACKGROUND

Diverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. We hypothesized that fecal samples representing the gut microbiota of rainbow trout could be associated with differential growth rates observed in fish breeding programs. If true, harnessing the functionality of this microbiota can improve the profitability of aquaculture. The first objective of this study was to test this hypothesis if gut microbiota is associated with fish growth rate (body weight). Four full-sibling families were stocked in the same tank and fed an identical diet. Two fast-growing and two slow-growing fish were selected from each family for 16S rRNA microbiota profiling. Microbiota diversity varies with different DNA extraction methods. The second objective of this study was to compare the effects of five commonly used DNA extraction methods on the microbiota profiling and to determine the most appropriate extraction method for this study. These methods were Promega-Maxwell, Phenol-chloroform, MO-BIO, Qiagen-Blood/Tissue, and Qiagen-Stool. Methods were compared according to DNA integrity, cost, feasibility and inter-sample variation based on non-metric multidimensional scaling ordination (nMDS) clusters.

RESULTS

Differences in DNA extraction methods resulted in significant variation in the identification of bacteria that compose the gut microbiota. Promega-Maxwell had the lowest inter-sample variation and was therefore used for the subsequent analyses. Beta diversity of the bacterial communities showed significant variation between breeding families but not between the fast- and slow-growing fish. However, an indicator analysis determined that cellulose, amylose degrading and amino acid fermenting bacteria (Clostridium, Leptotrichia, and Peptostreptococcus) are indicator taxa of the fast-growing fish. In contrary, pathogenic bacteria (Corynebacterium and Paeniclostridium) were identified as indicator taxa for the slow-growing fish.

CONCLUSION

DNA extraction methodology should be carefully considered for accurate profiling of the gut microbiota. Although the microbiota was not significantly different between the fast- and slow-growing fish groups, some bacterial taxa with functional implications were indicative of fish growth rate. Further studies are warranted to explore how bacteria are transmitted and potential usage of the indicator bacteria of fast-growing fish for development of probiotics that may improve fish health and growth.

Variability in snake skin microbial assemblages across spatial scales and disease states

Understanding how biological patterns translate into functional processes across different scales is a central question in ecology. Within a spatial context, extent is used to describe the overall geographic area of a study, whereas grain describes the overall unit of observation. This study aimed to characterize the snake skin microbiota (grain) and to determine host–microbial assemblage–pathogen effects across spatial extents within the Southern United States. The causative agent of snake fungal disease, Ophidiomyces ophiodiicola, is a fungal pathogen threatening snake populations. We hypothesized that the skin microbial assemblage of snakes differs from its surrounding environment, by host species, spatial scale, season, and in the presence of O. ophiodiicola. We collected snake skin swabs, soil samples, and water samples across six states in the Southern United States (macroscale extent), four Tennessee ecoregions (mesoscale extent), and at multiple sites within each Tennessee ecoregion (microscale extent). These samples were subjected to DNA extraction and quantitative PCR to determine the presence/absence of O. ophiodiicola. High-throughput sequencing was also utilized to characterize the microbial communities. We concluded that the snake skin microbial assemblage was partially distinct from environmental microbial communities. Snake host species was strongly predictive of the skin microbiota at macro-, meso-, and microscale spatial extents; however, the effect was variable across geographic space and season. Lastly, the presence of the fungal pathogen O. ophiodiicola is predictive of skin microbial assemblages across macro- and meso-spatial extents, and particular bacterial taxa associate with O. ophiodiicola pathogen load. Our results highlight the importance of scale regarding wildlife host–pathogen–microbial assemblage interactions.

The dendritic spine morphogenic effects of repeated cocaine use occur through the regulation of serum response factor signaling

The nucleus accumbens (NAc) is a primary brain reward region composed predominantly of medium spiny neurons (MSNs). In response to early withdrawal from repeated cocaine administration, de novo dendritic spine formation occurs in NAc MSNs. Much evidence indicates that this new spine formation facilitates the rewarding properties of cocaine. Early withdrawal from repeated cocaine also produces dramatic alterations in the transcriptome of NAc MSNs, but how such alterations influence cocaine's effects on dendritic spine formation remain unclear. Studies in non-neuronal cells indicate that actin cytoskeletal regulatory pathways in nuclei have a direct role in the regulation of gene transcription in part by controlling the access of co-activators to their transcription factor partners. In particular, actin state dictates the interaction between the serum response factor (SRF) transcription factor and one of its principal co-activators, MAL. Here we show that cocaine induces alterations in nuclear F-actin signaling pathways in the NAc with associated changes in the nuclear subcellular localization of SRF and MAL. Using in vivo optogenetics, the brain region-specific inputs to the NAc that mediate these nuclear changes are investigated. Finally, we demonstrate that regulated SRF expression, in turn, is critical for the effects of cocaine on dendritic spine formation and for cocaine-mediated behavioral sensitization. Collectively, these findings reveal a mechanism by which nuclear-based changes influence the structure of NAc MSNs in response to cocaine.

Next-to-Next-to-Leading-Order QCD Corrections to the Transverse Momentum Distribution of Weak Gauge Bosons

The transverse momentum spectra of weak gauge bosons and their ratios probe the underlying dynamics and are crucial in testing our understanding of the standard model. They are an essential ingredient in precision measurements, such as the W boson mass extraction. To fully exploit the potential of the LHC data, we compute the second-order [next-to-next-to-leading-order (NNLO)] QCD corrections to the inclusive-p_{T}^{W} spectrum as well as to the ratios of spectra for W^{-}/W^{+} and Z/W. We find that the inclusion of NNLO QCD corrections considerably improves the theoretical description of the experimental CMS data and results in a substantial reduction of the residual scale uncertainties.

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola

There is increasing concern regarding potential impacts of snake fungal disease (SFD), caused by Ophidiomyces ophiodiicola (Oo), on free-ranging snake populations in the eastern USA. The snake cutaneous microbiome likely serves as the first line of defense against Oo and other pathogens; however, little is known about microbial associations in snakes. The objective of this study was to better define the composition and immune function of the snake cutaneous microbiome. Eight timber rattlesnakes (Crotalus horridus) and four black racers (Coluber constrictor) were captured in Arkansas and Tennessee, with some snakes exhibiting signs of SFD. Oo was detected through real-time qPCR in five snakes. Additional histopathological techniques confirmed a diagnosis of SFD in one racer, the species' first confirmed case of SFD in Tennessee. Fifty-eight bacterial and five fungal strains were isolated from skin swabs and identified with Sanger sequencing. Non-metric multidimensional scaling and PERMANOVA analyses indicated that the culturable microbiome does not differ between snake species. Fifteen bacterial strains isolated from rattlesnakes and a single strain isolated from a racer inhibited growth of Oo in vitro. Results shed light on the culturable cutaneous microbiome of snakes and probiotic members that may play a role in fighting an emergent disease.

Editor's Choice - Frailty and the management of patients with acute cardiovascular disease: A position paper from the Acute Cardiovascular Care Association

Frailty is increasingly seen among patients with acute cardiovascular disease. A combination of an ageing population, improved disease survival, treatable long-term conditions as well as a greater recognition of the syndrome has accelerated the prevalence of frailty in the modern world. Yet, this has not been matched by an expansion of research. National and international bodies have identified acute cardiovascular disease in the frail as a priority area for care and an entity that requires careful clinical decisions, but there remains a paucity of guidance on treatment efficacy and safety, and how to manage this complex group. This position paper from the Acute Cardiovascular Care Association presents the latest evidence about frailty and the management of frail patients with acute cardiovascular disease, and suggests avenues for future research.

Sequence-based classification and identification of Fungi

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation

Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations.

Individual placement and support (IPS) for patients with offending histories: the IPSOH feasibility cluster randomised trial protocol

INTRODUCTION

People with involvement in forensic psychiatric services face many obstacles to employment, arising from their offending, as well as their mental health problems. This study aims to assess the feasibility of conducting a randomised controlled trial (RCT) to evaluate the effectiveness of individual placement and support (IPS), in improving employment rates and associated psychosocial outcomes in forensic psychiatric populations. IPS has been found consistently to achieve employment rates above 50% in psychiatric patients without a history of involvement in criminal justice services.

METHODS/DESIGN

This is a single-centre feasibility cluster RCT. Clusters will be defined according to clinical services in the community forensic services of Nottinghamshire Healthcare NHS Foundation Trust (NHCT). IPS will be implemented into 2 of the randomly assigned intervention clusters in the community forensic services of NHCT. A feasibility cluster RCT will estimate the parameters required to design a full RCT. The primary outcome is the proportion of people in open employment at 12-month follow-up. Secondary outcome measures will include employment, educational activities, psychosocial and economic outcomes, as well as reoffending rates. Outcome measures will be recorded at baseline, 6 months and 12 months. In accordance with the UK Medical Research Council guidelines on the evaluation of complex interventions, a process evaluation will be carried out; qualitative interviews with patients and staff will explore general views of IPS as well as barriers and facilitators to implementation. Fidelity reviews will assess the extent to which the services follow the principles of IPS prior, during and at the end of the trial.

ETHICS AND DISSEMINATION

Ethical approval was obtained from the East Midlands Research Ethics Committee-Nottingham 1 (REC reference number 15/EM/0253). Final and interim reports will be prepared for project funders, the study sponsor and clinical research network. Findings will be disseminated through peer-reviewed journals, conferences and event presentations.

TRIAL REGISTRATION NUMBER

NCT02442193; Pre-results.

Recommendations of generic names in Diaporthales competing for protection or use

In advancing to one name for fungi, this paper treats generic names competing for use in the order Diaporthales (Ascomycota, Sordariomycetes) and makes a recommendation for the use or protection of one generic name among synonymous names that may be either sexually or asexually typified. A table is presented that summarizes these recommendations. Among the genera most commonly encountered in this order, Cytospora is recommended over Valsa and Diaporthe over Phomopsis. New combinations are introduced for the oldest epithet of important species in the recommended genus. These include Amphiporthe tiliae, Coryneum lanciforme, Cytospora brevispora, C. ceratosperma, C. cinereostroma, C. eugeniae, C. fallax, C. myrtagena, Diaporthe amaranthophila, D. annonacearum, D. bougainvilleicola, D. caricae-papayae, D. cocoina, D. cucurbitae, D. juniperivora, D. leptostromiformis, D. pterophila, D. theae, D. vitimegaspora, Mastigosporella georgiana, Pilidiella angustispora, P. calamicola, P. pseudogranati, P. stromatica, and P. terminaliae.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest

The flow of energy within an ecosystem can be considered either top-down, where predators influence consumers, or bottom-up, where producers influence consumers. Plethodon cinereus (Red-backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, U.S.A. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics-based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.

Database URL:http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353

Re-evaluating niche conservatism versus divergence in the Woodland Salamander genus Plethodon: a case study of the parapatric members of the Plethodon glutinosus species complex

The Woodland Salamander genus Plethodon Tschudi, 1838, consists of terrestrial lungless salamanders, has been cited as an exemplar of a lineage characterized by niche conservatism. This conclusion has contributed to broader hypotheses dealing with the role of niche conservatism in speciation and the maintenance of species diversity. We re-evaluated these salamanders using newly published techniques designed to detect niche conservatism versus niche divergence using computer-based niche modeling and spatial analysis within a phylogenetic framework. We specifically studied parapatric neighbors in the species complex of Plethodon glutinosus (Green, 1818) to determine if there is evidence of a role for niche divergence at speciation or if niche conservatism characterizes the complex as has been reported for the larger genus. We found that new statistical approaches yield different results from earlier work, suggesting that niche divergence has been a much more important player in the speciation process than has heretofore been understood. Although different parts of the overall Plethodon phylogeny may be characterized by different rates of niche evolution, the rapidly burgeoning area of research centered on niche conservatism appears to be in a state of flux with regards to methods that give consistently repeatable results.

New molecular markers for fungal phylogenetics: two genes for species-level systematics in the Sordariomycetes (Ascomycota)

Although significant progress has been made resolving deep branches of the fungal tree of life, many fungal systematists are interested in species-level questions to both define species and assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic biologists for developing new phylogenetic markers that better represent the whole genome. Here we report primers for two newly identified single-copy protein-coding genes, FG1093 and MS204, for use with ascomycetes. Although fungi were the focus of this study, this methodological approach could be easily applied to marker development for studies of other organisms. The tests used here to assess phylogenetic informativeness are computationally rapid, require only rudimentary datasets to evaluate existing or newly developed markers, and can be applied to other non-model organisms to assist in experimental design of phylogenetic studies. Phylogenetic utility of the markers was tested in two genera, Gnomoniopsis and Ophiognomonia (Gnomoniaceae, Diaporthales). The phylogenetic performance of β-tubulin, ITS, and tef-1α was compared with FG1093 and MS204. Phylogenies inferred from FG1093 and MS204 were largely in agreement with β-tubulin, ITS, and tef-1α although some topological conflict was observed. Resolution and support for branches differed based on the combination of markers used for each genus. Based on two independent tests of phylogenetic performance, FG1093 and MS204 were determined to be equal to or better than β-tubulin, ITS, and tef-1α in resolving species relationships. Differences were found in site-specific rate of evolution in all five markers. In addition, isolates from 15 orders and 22 families of Ascomycota were screened using primers for FG1093 and MS204 to demonstrate primer utility across a wide diversity of ascomycetes. The primer sets for the newly identified genes FG1093 and MS204 and methods used to develop them are useful additions to the ascomycete systematists' toolbox.

d3-GHR genotype does not explain heterogeneity in GH responsiveness in hypopituitary adults

OBJECTIVE

Heterogeneity in growth hormone (GH) responsiveness in adult hypopituitary patients receiving recombinant human GH (rhGH) is poorly understood; doses vary up to fourfold between individuals. Deletion of exon 3 in the GH receptor (d3-GHR) has been linked to enhanced rhGH responsiveness in children. We investigated the role of the d3-GHR polymorphism in determining adult rhGH responsiveness.

METHODS

One hundred and ninety-four patients treated with an identical rhGH dosing protocol in a single centre were genotyped for the d3-GHR, and the results correlated with changes in serum IGF-I and clinical parameters of GH responsiveness after 6 and 12 months of GH replacement therapy.

RESULTS

Allele frequencies for homozygous full length (fl/fl), heterozygous d3 (fl/d3) and homozygous d3 (d3/d3) were 52%, 38.7% and 9.3%, respectively, and were in Hardy-Weinberg equilibrium. Baseline IGF-I and DeltaIGF-I at 6 months were comparable between groups. DeltaIGF-I at 12 months was significantly greater in the d3/d3 group (P = 0.028). No difference was detected between fl/d3 and fl/fl groups. Regression analyses of DeltaIGF-I at 12 months and DeltaIGF-I/rhGH dose confirmed a significant relationship of d3/d3 genotype on rhGH response. There was no difference between groups in maintenance rhGH dose between genotypes.

CONCLUSION

Homozygosity for d3-GHR confers a marginal increase in GH responsiveness at 12 months but without a detectable change in maintenance rhGH dose required. Both d3 alleles are required to achieve this response; given that only 10% of the population are d3 homozygotes, the d3GHR does not explain the marked heterogeneity of GH responsiveness in hypopituitary adults.

Improving survival in the 6 months after diagnosis of heart failure in the past decade: population-based data from the UK

OBJECTIVE

To investigate the secular trend in survival after a new diagnosis of heart failure in the UK population.

DESIGN AND SETTING

Comparison of all-cause mortality in the 6 months after diagnosis of heart failure in population-based studies in the south east of England in 2004-5 (Hillingdon-Hastings Study) and 1995-7 (Hillingdon-Bromley Studies).

PARTICIPANTS

396 patients in the 2004-5 cohort and 552 patients in the 1995-7 cohort with incident (new) heart failure.

MAIN OUTCOME MEASURES

All-cause mortality.

RESULTS

All-cause mortality rates were 6% (95% CI 3% to 8%) at 1 month, 11% (8% to 14%) at 3 months and 14% (11% to 18%) at 6 months in the 2004-5 cohort compared with 16% (13% to 20%), 22% (19% to 25%) and 26% (22% to 29%), respectively, in the 1995-7 cohort (difference between the two cohorts, p<0.001). The difference in survival was not explained by any difference in the demographics or severity of heart failure at presentation. There was a difference at baseline and thereafter in the use of neurohormonal antagonists (beta-blockers and angiotensin-converting enzyme inhibitors).

CONCLUSIONS

Although early mortality remains high among patients with newly diagnosed heart failure in the UK general population, there is strong evidence of a marked improvement in survival from 1995-7 to 2004-5, perhaps partly explained by an increased usage of neurohormonal antagonists.

Pooled faecal culture for the detection of Mycobacterium avium subsp paratuberculosis in goats

OBJECTIVE

To evaluate pooled faecal culture for herd diagnosis of caprine Johne's disease and relate these findings to faecal shedding rates of Mycobacterium avium subsp paratuberculosis (Map).

DESIGN

Radiometric broth culture was applied to several pooling dilutions, and shedding rates were estimated from a regression equation based on bacterial growth rates and known processing losses during radiometric culture.

PROCEDURE

Sixteen faecal samples from goats naturally infected with sheep (n = 3) or cattle (n = 13) strains of Map, were diluted in normal goat faeces from 1 in 5 to 1 in 50. Cultures were confirmed by IS900 polymerase chain reaction and restriction endonuclease analysis, and mycobactin dependency. The numbers of viable Map in the culture inocula were determined by endpoint titration (most probable number) of nine samples and related to a cumulative growth index.

RESULTS

A pooling dilution of 1 in 25 with an incubation period of 10 weeks detected 13 of 16 culture positive goats, all shedding > or = 2 x 10(4) Map per gram of faeces. Two samples containing very low numbers of Map (< 2 x 10(3)/g) were only culture positive from undiluted faeces. Thirteen of 16 goats were considered to be shedding low to moderate concentrations of Map (< 2 x 10(5)/g faeces).

CONCLUSIONS

These data support a pooling dilution of 1 in 25 for application of pooled faecal culture as a diagnostic tool in caprine Johne's disease control. A test based on this dilution would reduce laboratory costs of whole herd testing in goats by approximately 40% relative to serology and 75 to 90% relative to individual faecal culture.

A case of aggressive multiple metachronous central giant cell granulomas of the jaws: differential diagnosis and management options

We describe multiple metachronous central giant cell granulomas in a 62-year-old man who has a first degree relative with a history of a solitary central giant cell granulomas. The patient presented in 1997 with a large central giant cell granuloma of the right maxilla which was treated with a partial maxillectomy. A small recurrence was then identified and the successful management of this is described. The patient has also a histologically confirmed central giant cell granuloma previously removed from the right body of the mandible and the left angle of the mandible. The differential diagnosis of multiple central giant cell granulomas of the jaw is considered. It is possible that the present case may indeed represent a new syndrome or subtype of multiple central giant cell granulomas. The problem of treating such aggressive sub-types of giant cell granulomas is also addressed in the context of recent advances of surgical and medical management.

Primary Orbital Ewing Sarcoma in a Middle-Aged Man

A 54-year-old man presented with a painful left proptosis and a soft tissue mass at the inferolateral aspect of the left orbit with bone involvement. There was no clinical or investigational evidence of systemic disease. Both light microscopy and immunohistochemistry were required for the diagnosis of Ewing sarcoma. After failure of chemotherapy alone, management included extensive surgical excision and postoperative adjuvant radiotherapy and chemotherapy. Despite intervention, the patient died of widespread metastatic disease 17 months after initial presentation. Although rare, Ewing sarcoma should be included in the differential diagnosis of uniform round cell orbital tumors in adults.

Oral mucosal immunology: an overview

The primary function of the immune system of the mouth is to protect the teeth, jaws, gingivae and oral mucosa against infection. These host defences vary in the different oral microenvironments or domains represented by the oral mucosa, saliva and gingival crevice. This review aims to consider and contrast the main immune components in each domain and cites examples of oral diseases where the immune response is defective.

Tongue cancer: Do patients younger than 40 do worse?

BACKGROUND

Debate continues as to whether being young confers a worse prognosis for patients with squamous cell carcinoma of the tongue. Recent papers have provided conflicting views in this debate. In this study we aimed to investigate if young age at the time of diagnosis of squamous cell carcinoma of the tongue confers a worse prognosis.

METHODS

Eligible patients were identified through the computer database of the Department of Radiation Oncology, Westmead Hospital, Sydney. All eligible patients were treated with radical intent. Using age 40 as a cut off multivariate and survival analysis was undertaken to compare age groups.

RESULTS

Median age at diagnosis was 60 years (range, 19-86 years) in 84 males (65 per cent) and 45 females (35 per cent). Median follow-up time was 43 months (range, 2.3-203 months). Fifteen patients (12 per cent) were aged <40 years. On univariate analysis stage and age were significant determinants of disease-specific survival. There was no difference in overall survival between the young (<40 years) and middle-aged groups (40-60 years). However, the young and the middle aged were both more likely to survive than the older age group (>60 years). On multivariate analysis age remained a significant factor for determining disease-specific survival, with the older age group 2.9 times more likely to die than the younger groups.

CONCLUSION

Young age (<40 years) did not portend to worse survival in comparison to older tongue cancer patients.

Induction of contact-dependent endothelial apoptosis by osteosarcoma cells suggests a role for endothelial cell apoptosis in blood-borne metastasis

Although tumour cells are believed to migrate between endothelial cells early in metastasis, the possibility remains that endothelial apoptosis may also contribute to the tumour's breach of the vascular barrier. Although seemingly inconsistent with tumour angiogenesis, one publication describes the induction of contact-dependent apoptosis in cultured endothelium by tumour cells. The cell culture data are, however, open to challenge on technical grounds while there are no confirmatory reports. The present paper describes experiments overcoming these limitations. SAOS-2 human osteosarcoma cells and two rat carcinoma cell lines were co-cultured with human umbilical vein endothelial cells (HUVECs) and cultures labelled by surface lectin histochemistry for endothelium. The HUVEC culture density was determined and SAOS-2 cells, but not rat carcinoma cells, were found significantly to reduce HUVEC survival despite the release of potent growth factors as determined in separate experiments with tumour cell conditioned medium. Lectin labelling combined with light microscopy, transmission electron microscopy, flow cytometry for both lectin binding and DNA content, and DNA gel electrophoresis of SAOS-2/HUVEC co-cultures revealed extensive HUVEC apoptosis. These findings indicate contact-dependent endothelial apoptosis by SAOS-2, while this activity appeared weaker and overwhelmed by HUVEC proliferation with rat carcinoma cells. Importantly, this study supports the suggestion that endothelial apoptosis may be important for metastasis and suggests a complex interplay between endothelial proliferation and apoptosis in tumours.

Classical and variant Creutzfeldt-Jakob diseases and their potential impact on the practice of clinical dentistry in Australia

Following recent published evidence regarding the experimental transmission of prion diseases via blood transfusion, dental practitioners have expressed their concern about the potential impact of these transmissible spongiform encephalopathies on dental care provision. This review provides updated information on Creutzfeldt-Jakob disease and related disorders and highlights their potential significance for the practice of clinical dentistry. The current guidelines in Australia relating to infection control and clinical dental procedures are discussed together with recommended guidelines and considerations from the United Kingdom and the World Health Organization (WHO).