The culturable mycobiota associated with three Atlantic sponges, including two new species: Thelebolus balaustiformis and T. spongiae.

Covering 70 % of Earth, oceans are at the same time the most common and the environment least studied by microbiologists. Considering the large gaps in our knowledge on the presence of marine fungi in the oceans, the aim of this research was to isolate and identify the culturable fungal community within three species of sponges, namely Dysidea fragilis, Pachymatisma johnstonia and Sycon ciliatum, collected in the Atlantic Ocean and never studied for their associated mycobiota. Applying different isolation methods, incubation temperatures and media, and attempting to mimic the marine and sponge environments, were fundamental to increase the number of cultivable taxa. Fungi were identified using a polyphasic approach, by means of morpho-physiological, molecular and phylogenetic techniques. The sponges revealed an astonishing fungal diversity represented by 87 fungal taxa. Each sponge hosted a specific fungal community with more than half of the associated fungi being exclusive of each invertebrate. Several species isolated and identified in this work, already known in terrestrial environment, were first reported in marine ecosystems (21 species) and in association with sponges (49 species), including the two new species Thelebolus balaustiformis and Thelebolus spongiae, demonstrating that oceans are an untapped source of biodiversity.

Human metapneumovirus-associated respiratory tract infections in the Republic of Ireland during the influenza season of 2003-2004.

Human metapneumovirus (hMPV) is a newly identified paramyxovirus that has been associated with respiratory tract illness in children aged < 5 years, the elderly, and immunocompromised patients. This study determined the frequency of respiratory tract infections (RTIs) associated with hMPV in the Republic of Ireland. Bronchoalveolar lavage (BAL) samples from 168 adult patients and respiratory specimens from 122 children aged < 5 years were collected between September 2003 and May 2004. The virus was detected by reverse-transcription (RT)-PCR using hMPV polymerase (L) and matrix (M)-specific primers in four (2.4%) of 171 BAL specimens obtained from 168 adults. No other respiratory virus was detected in these specimens, and no hMPV RNA was detected in respiratory specimens from children during the same time period. In all four adult cases, two of whom had underlying disease, hMPV was associated with mild, self-limiting upper RTIs. The most common clinical findings included fever (3/4 patients), cough (4/4) and rhinorrhoea (3/4). No patient died as a result of these RTI episodes. Phylogenetic analysis was performed using the amplified regions of the M and fusion (F) genes of hMPV. The Irish isolates belonged to cluster 1B, and did not show a separate Irish sub-lineage.

DPRml: distributed phylogeny reconstruction by maximum likelihood.

MOTIVATION: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to address the huge computational requirements of maximum likelihood. We express a number of concerns about the current set of parallel phylogenetic programs which are currently severely limiting the widespread availability and use of parallel computing in maximum likelihood-based phylogenetic analysis. RESULTS: We have identified the suitability of phylogenetic analysis to large-scale heterogeneous distributed computing. We have completed a distributed and fully cross-platform phylogenetic tree building program called distributed phylogeny reconstruction by maximum likelihood. It uses an already proven maximum likelihood-based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations. It offers one of the most extensive sets of DNA substitution models currently available. We are the first, to our knowledge, to report the completion of a distributed phylogenetic tree building program that can achieve near-linear speedup while only using the idle clock cycles of machines. For those in an academic or corporate environment with hundreds of idle desktop machines, we have shown how distributed computing can deliver a 'free' ML supercomputer.