Flagging greens: hydrobiid snails as substrata for the development of green algal mats (Enteromorpha spp.) on tidal flats of North Atlantic coasts

During the past 3 decades, dense mats of green algae (especially Enteromorpha spp.) have been recorded regularly from tidal flats worldwide. The development of green algal mats on tidal flats may be initiated by overwintering and regrowth of adult plants or by the formation and release of small propagules, i.e. vegetative fragments, zoospores and zygotes. On soft sediments, macroinvertebrates may constitute prime substrata for germination of algal spores. Hydrobud (mud-) snails are widespread along North Atlantic soft sediment shores and were identified previously as important substrata for Enteromorpha spp. germlings in 1 of our study areas. To test the generality of this phenomenon, we investigated the presence of Enteromorpha spp. gerrnlings attached to hydrobud snails from November 1995 to December 1996 on 6 tidal flats of North Atlantic coasts (Tralebergslule, Sweden; Konigshafen Bay, Germany; Mondego Estuary, Portugal; Ria Formosa, Portugal; Cole Harbour, Nova Scotia, Canada; Lowes Cove, Maine, USA). With 1 exception, hydrobiid snails were present in all areas studied, and intensive growth of Enteromorpha spp. occurred during summer. Throughout winter 1995/96, hardly any Enteromorpha spp. gerrnlings were found on snail shells, but over the following months germlings developed on up to 60% of the hydrobiid snails present. In 2 areas (Konigshafen, Germany; Lowes Cove, USA), germhng abundance on hydrobuds began to rise before the peak of green algal mat development. In Tralebergskile, Sweden, high mat abundance occurred simultaneous to and after increased germling abundance on Hydrobia ulvae. Densities of snails were very low, however, and hydrobuds appeared to be unimportant as substratum. No clear temporal pattern between high germling abundance on snails followed by mat development was found in the other 3 study areas (Ria Formosa, Portugal; Mondego Estuary, Portugal; Cole Harbour, Canada). In Lowes Cove, USA, gerrnlings and juveniles of Enteromorpha spp. first grew at the site with high Hydrobia abundance and were subsequently drifted to another site where they developed into full mats. We conclude that initiation of green algal mats by germination on Hydrobia spp. may be a general phenomenon, but that other modes of development also occur frequently. Pelagic dnft of overwintering thalli to new sites, followed by prolific growth, might be of similar or greater importance

High-throughput screening of tick-borne pathogens in Europe

Due to increased travel, climatic, and environmental changes, the incidence of tick-borne disease in both humans and animals is increasing throughout Europe. Therefore, extended surveillance tools are desirable. To accurately screen tick-borne pathogens (TBPs), a large scale epidemiological study was conducted on 7050 Ixodes ricinus nymphs collected from France, Denmark, and the Netherlands using a powerful new high-throughput approach. This advanced methodology permitted the simultaneous detection of 25 bacterial, and 12 parasitic species (including; Borrelia, Anaplasma, Ehrlichia, Rickettsia, Bartonella, Candidatus Neoehrlichia, Coxiella, Francisella, Babesia, and Theileria genus) across 94 samples. We successfully determined the prevalence of expected (Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, Rickettsia helvetica, Candidatus Neoehrlichia mikurensis, Babesia divergens, Babesia venatorum), unexpected (Borrelia miyamotoi), and rare (Bartonella henselae) pathogens in the three European countries. Moreover we detected Borrelia spielmanii, Borrelia miyamotoi, Babesia divergens, and Babesia venatorum for the first time in Danish ticks. This surveillance method represents a major improvement in epidemiological studies, able to facilitate comprehensive testing of TBPs, and which can also be customized to monitor emerging diseases

The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research.

The ISB Cancer Genomics Cloud (ISB-CGC) is one of three pilot projects funded by the National Cancer Institute to explore new approaches to computing on large cancer datasets in a cloud environment. With a focus on Data as a Service, the ISB-CGC offers multiple avenues for accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GENCODE and COSMIC using the Google Cloud Platform. The open approach allows researchers to choose approaches best suited to the task at hand: from analyzing terabytes of data using complex workflows to developing new analysis methods in common languages such as Python, R, and SQL; to using an interactive web application to create synthetic patient cohorts and to explore the wealth of available genomic data. Links to resources and documentation can be found at www.isb-cgc.or

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types