Differing preferences of Antarctic soil nematodes for microbial prey

We tested the preferences of three nematode taxa, Geomonhystera villosa, Plectus spp. and Teratocephalus spp., extracted from moss at Signy Island in the Maritime Antarctic, for two microalgae, three microfungi and six heterotrophic bacteria, each also from soils at Signy Island. Choice test experiments on water agar medium, in which nematodes were enumerated in wells containing microbes at 24 and 48 h, indicated that there were differing preferences between nematodes for distinct prey. G. villosa was significantly attracted to the alga Chlorella cf. minutissima and the fungus Mortierella hyalina, and was more attracted to all algae and fungi than either of the other two nematodes. Both G. villosa and Teratocephalus spp. were attracted to an actinobacterium. Plectus spp. were significantly attracted to the alga Stichococcus bacillaris and bacteria with close taxonomic affinities to Arthrobacter, Pseudomonas and Polaromonas. Experiments using 0.5 μm diameter fluorescent beads indicated significantly increased ingestion by nematodes in the presence of each of these microbes compared with controls, except by Plectus spp. in the presence of S. bacillaris. We conclude that complex trophic interactions may occur in apparently simple Antarctic soil food webs

Discrete taxa of saprotrophic fungi respire different ages of carbon from Antarctic soils

Different organic compounds have distinct residence times in soil and are degraded by specific taxa of saprotrophic fungi. It hence follows that specific fungal taxa should respire carbon of different ages from these compounds to the atmosphere. Here, we test whether this is the case by radiocarbon (14C) dating CO2 evolved from two gamma radiation-sterilised maritime Antarctic soils inoculated with pure single cultures of four fungi. We show that a member of the Helotiales, which accounted for 41–56% of all fungal sequences in the two soils, respired soil carbon that was aged up to 1,200 years BP and which was 350–400 years older than that respired by the other three taxa. Analyses of the enzyme profile of the Helotialean fungus and the fluxes and δ13C values of CO2 that it evolved suggested that its release of old carbon from soil was associated with efficient cellulose decomposition. Our findings support suggestions that increases in the ages of carbon respired from warmed soils may be caused by changes to the abundances or activities of discrete taxa of microbes, and indicate that the loss of old carbon from soils is driven by specific fungal taxa

Widespread association between the ericoid mycorrhizal fungus Rhizoscyphus ericae and a leafy liverwort in the maritime and sub-Antarctic

A recent study identified a fungal isolate from the Antarctic leafy liverwort Cephaloziella varians as the ericoid mycorrhizal associate Rhizoscyphus ericae. However, nothing is known about the wider Antarctic distribution of R. ericae in C. varians, and inoculation experiments confirming the ability of the fungus to form coils in the liverwort are lacking. Using direct isolation and baiting with Vaccinium macrocarpon seedlings, fungi were isolated from C. varians sampled from eight sites across a 1875-km transect through sub- and maritime Antarctica. The ability of an isolate to form coils in aseptically grown C. varians was also tested. Fungi with 98–99% sequence identity to R. ericae internal transcribed spacer (ITS) region and partial large subunit ribosomal (r)DNA sequences were frequently isolated from C. varians at all sites sampled. The EF4/Fung5 primer set did not amplify small subunit rDNA from three of five R. ericae isolates, probably accounting for the reported absence of the fungus from C. varians in a previous study. Rhizoscyphus ericae was found to colonize aseptically-grown C. varians intracellularly, forming hyphal coils. This study shows that the association between R. ericae and C. varians is apparently widespread in Antarctica, and confirms that R. ericae is at least in part responsible for the formation of the coils observed in rhizoids of field-collected C. varians

Liverworts frequently form mycothalli on Spitsbergen in the High Arctic

Mycothalli, symbioses between liverworts and soil fungi, have not previously been recorded in the Arctic. Here, 13 species of leafy liverwort from west Spitsbergen in the High Arctic are examined for the symbiosis using epifluorescence microscopy and sequencing of fungal ribosomal (r)RNA genes amplified from plant tissues. Microscopy showed that intracellular hyphal coils, key indicators of the symbiosis, were frequent (>40% stem length colonized) in nine species of liverwort in the families Anastrophyllaceae, Lophoziaceae, Cephaloziellaceae, Cephaloziaceae and Scapaniaceae, with hyphae occurring frequently (>40% cells occupied) in the rhizoids of 10 species in the same families. Dark septate hyphae, apparently formed by ascomycetes, were frequent on the stems of members of the Anastrophyllaceae, Cephaloziellaceae and Cephaloziaceae, and typically those growing on acidic mine tailings. Sequencing of fungal rRNA genes showed the presence of nine distinct groups (based on a 3% cut-off for ITS sequence divergence) of the basidiomycete Serendipita in the Anastrophyllaceae and Lophoziaceae, with ordinations and correlative analyses showing the presence of the genus to be positively associated with the frequency of hyphal coils, the occurrence of which was positively associated with edaphic factors (soil δ15N value and concentrations of moisture, nitrogen, carbon and organic matter). We propose that the frequency of mycothalli in leafy liverworts on west Spitsbergen, which is an order of magnitude higher than at lower latitudes, may arise from benefits conferred by mycobionts on their hosts in the harsh environment of the High Arctic

Allelic loss on chromosome band 18p11.3 occurs early and reveals heterogeneity in breast cancer progression

We examined the stage specificity and heterogeneity of 18p11 alterations in a series of tumors representing 96 microdissected samples. Significant loss of heterozygosity (LOH) (63%) was found, with 56% occurring early in ductal carcinoma in situ. Although most cases indicated LOH was clonally inherited, heterogeneity for 18p LOH occurred in 27% of tumors. When compared with other LOH data, 18p LOH was found in conjunction with allelic deletion on 3p, 9p, 17p and 17q, while 13q, 16q, and 11p were less frequently associated. These analyses suggest chromosome 18p11 alteration is a common and early event in breast disease

Experimental warming increases fungal alpha diversity in an oligotrophic maritime Antarctic soil

The climate of maritime Antarctica has altered since the 1950s. However, the effects of increased temperature, precipitation and organic carbon and nitrogen availability on the fungal communities inhabiting the barren and oligotrophic fellfield soils that are widespread across the region are poorly understood. Here, we test how warming with open top chambers (OTCs), irrigation and the organic substrates glucose, glycine and tryptone soy broth (TSB) influence a fungal community inhabiting an oligotrophic maritime Antarctic fellfield soil. In contrast with studies in vegetated soils at lower latitudes, OTCs increased fungal community alpha diversity (Simpson’s index and evenness) by 102–142% in unamended soil after 5 years. Conversely, OTCs had few effects on diversity in substrate-amended soils, with their only main effects, in glycine-amended soils, being attributable to an abundance of Pseudogymnoascus. The substrates reduced alpha and beta diversity metrics by 18–63%, altered community composition and elevated soil fungal DNA concentrations by 1–2 orders of magnitude after 5 years. In glycine-amended soil, OTCs decreased DNA concentrations by 57% and increased the relative abundance of the yeast Vishniacozyma by 45-fold. The relative abundance of the yeast Gelidatrema declined by 78% in chambered soil and increased by 1.9-fold in irrigated soil. Fungal DNA concentrations were also halved by irrigation in TSB-amended soils. In support of regional- and continental-scale studies across climatic gradients, the observations indicate that soil fungal alpha diversity in maritime Antarctica will increase as the region warms, but suggest that the accumulation of organic carbon and nitrogen compounds in fellfield soils arising from expanding plant populations are likely, in time, to attenuate the positive effects of warming on diversity. Antarctica, climate warming, open top chambers (OTCs), organic carbon, organic nitrogen, soil fungal community diversity, yeastspublishedVersio

Experimental warming increases fungal alpha diversity in an oligotrophic maritime Antarctic soil

The climate of maritime Antarctica has altered since the 1950s. However, the effects of increased temperature, precipitation and organic carbon and nitrogen availability on the fungal communities inhabiting the barren and oligotrophic fellfield soils that are widespread across the region are poorly understood. Here, we test how warming with open top chambers (OTCs), irrigation and the organic substrates glucose, glycine and tryptone soy broth (TSB) influence a fungal community inhabiting an oligotrophic maritime Antarctic fellfield soil. In contrast with studies in vegetated soils at lower latitudes, OTCs increased fungal community alpha diversity (Simpson’s index and evenness) by 102–142% in unamended soil after 5 years. Conversely, OTCs had few effects on diversity in substrate-amended soils, with their only main effects, in glycine-amended soils, being attributable to an abundance of Pseudogymnoascus. The substrates reduced alpha and beta diversity metrics by 18–63%, altered community composition and elevated soil fungal DNA concentrations by 1–2 orders of magnitude after 5 years. In glycine-amended soil, OTCs decreased DNA concentrations by 57% and increased the relative abundance of the yeast Vishniacozyma by 45-fold. The relative abundance of the yeast Gelidatrema declined by 78% in chambered soil and increased by 1.9-fold in irrigated soil. Fungal DNA concentrations were also halved by irrigation in TSB-amended soils. In support of regional- and continental-scale studies across climatic gradients, the observations indicate that soil fungal alpha diversity in maritime Antarctica will increase as the region warms, but suggest that the accumulation of organic carbon and nitrogen compounds in fellfield soils arising from expanding plant populations are likely, in time, to attenuate the positive effects of warming on diversity. Antarctica, climate warming, open top chambers (OTCs), organic carbon, organic nitrogen, soil fungal community diversity, yeastspublishedVersio

A Multi-level Approach for Identifying Process Change in Cancer Pathways

An understudied challenge within process mining is the area of process change over time. This is a particular concern in healthcare, where patterns of care emerge and evolve in response to individual patient needs and through complex interactions between people, process, technology and changing organisational structure. We propose a structured approach to analyse process change over time suitable for the complex domain of healthcare. Our approach applies a qualitative process comparison at three levels of abstraction: a holistic perspective summariz-ing patient pathways (process model level), a middle level perspective based on activity sequences for individuals (trace level), and a fine-grained detail focus on activities (activity level). Our aim is to identify points in time where a process changed (detection), to localise and characterise the change (localisation and characterisation), and to understand process evolution (unravelling). We illus-trate the approach using a case study of cancer pathways in Leeds Cancer Centre where we found evidence of agreement in process change identified at the pro-cess model and activity levels, but not at the trace level. In the experiment we show that this qualitative approach provides a useful understanding of process change over time. Examining change at the three levels provides confirmatory ev-idence of process change where perspectives agree, while contradictory evidence can lead to focused discussions with domain experts. The approach should be of interest to others dealing with processes that undergo complex change over time

Amblyopia and quality of life: a systematic review

Background/Aims Amblyopia is a common condition which can affect up to 5% of the general population. The health-related quality of life (HRQoL) implications of amblyopia and/or its treatment have been explored in the literature. Methods A systematic literature search was undertaken (16th-30th January 2007) to identify the HRQoL implications of amblyopia and/or its treatment. Results A total of 25 papers were included in the literature review. The HRQoL implications of amblyopia related specifically to amblyopia treatment, rather than the condition itself. These included the impact upon family life; social interactions; difficulties undertaking daily activities; and feelings and behaviour. The identified studies adopted a number of methodologies. The study populations included; children with the condition; parents of children with amblyopia; and adults who had undertaken amblyopia treatment as a child. Some studies developed their own measures of HRQoL, and others determined HRQoL through proxy measures. Conclusions The reported findings of the HRQoL implications are of importance when considering the management of cases of amblyopia. Further research is required to assess the immediate and long-term effects of amblyopia and/or its treatment upon HRQoL using a more standardised approach

Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils

The ever increasing microbial resistome means there is an urgent need for new antibiotics. Metagenomics is an underexploited tool in the field of drug discovery. In this study we aimed to produce a new updated assay for the discovery of biosynthetic gene clusters encoding bioactive secondary metabolites. PCR assays targeting the polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) were developed. A range of European soils were tested for their biosynthetic potential using clone libraries developed from metagenomic DNA. Results revealed a surprising number of NRPS and PKS clones with similarity to rare Actinomycetes. Many of the clones tested were phylogenetically divergent suggesting they were fragments from novel NRPS and PKS gene clusters. Soils did not appear to cluster by location but did represent NRPS and PKS clones of diverse taxonomic origin. Fosmid libraries were constructed from Cuban and Antarctic soil samples; 17 fosmids were positive for NRPS domains suggesting a hit rate of less than 1 in 10 genomes. NRPS hits had low similarities to both rare Actinobacteria and Proteobacteria; they also clustered with known antibiotic producers suggesting they may encode for pathways producing novel bioactive compounds. In conclusion we designed an assay capable of detecting divergent NRPS and PKS gene clusters from the rare biosphere; when tested on soil samples results suggest the majority of NRPS and PKS pathways and hence bioactive metabolites are yet to be discovere