In situ observations of fish associated with coral reefs off Ireland

The abundance and behaviour of fish on and around coral reefs at Twin Mounds and Giant Mounds, carbonate mounds located on the continental shelf off Ireland (600-1100. m), were studied using two Remotely Operated Vehicle (ROV) dives. We recorded 30 fish taxa on the dives, together with three species of Scleractinia (Lophelia pertusa, Madrepora oculata and Desmophyllum cristagalli) and a diverse range of other corals (Antipatharia, Alcyonacea, and Stylasteridae). Stands of live coral provided the only habitat in which Guttigadus latifrons was observed whereas Neocyttus helgae was found predominantly on structural habitats provided by dead coral. Significantly more fish were found on structurally complex coral rubble habitats than on flatter areas where coral rubble was clogged with sand. The most common species recorded was Lepidion eques (2136 individuals), which always occurred a few cm above bottom and was significantly more active on the reefs than on sedimentary habitats. Synaphobranchus kaupii (1157 indiv.). , N. helgae (198 indiv.) and Micromesistius poutassou (116 indiv.) were also common; S. kaupii did not exhibit habitat-related differences in behaviour, whilst N. helgae was more active over the reefs and other structured habitats whereas M. poutassou was more active with decreasing habitat complexity. Trawl damage and abandoned fishing gear was observed at both sites. We conclude that Irish coral reefs provide complex habitats that are home to a diverse assemblage of fish utilising the range of niches occurring both above and within the reef structure. © 2011 Elsevier Ltd

Isolation and characterization of a laminin-binding protein from rat and chick muscle.

A major laminin-binding protein (LBP), distinct from previously described LBPs, has been isolated from chick and rat skeletal muscle (Mr 56,000 and 66,000, respectively). The purified LBPs from the two species were shown to be related antigenically and to have similar NH2-terminal amino acid sequences and total amino acid compositions. Protein blots using laminin and laminin fragments provided evidence that this LBP interacts with the major heparin-binding domain, E3, of laminin. Studies on the association of this LBP with muscle membrane fractions and reconstituted lipid vesicles indicate that this protein can interact with lipid bilayers and has properties of a peripheral, not an integral membrane protein. These properties are consistent with its amino acid sequence, determined from cDNAs (Clegg et al., 1988). Examination by light and electron microscopy of the LBP antigen distribution in skeletal muscle indicated that the protein is localized primarily extracellularly, near the extracellular matrix and myotube plasmalemma. While a form of this LBP has been identified in heart muscle, it is present at low or undetectable levels in other tissues examined by immunocytochemistry indicating that it is probably a muscle-specific protein. As this protein is localized extracellularly and can bind to both membranes and laminin, it may mediate myotube interactions with the extracellular matrix

BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly.

BackgroundThe problem of de-novo assembly for metagenomes using only long reads is gaining attention. We study whether post-processing metagenomic assemblies with the original input long reads can result in quality improvement. Previous approaches have focused on pre-processing reads and optimizing assemblers. BIGMAC takes an alternative perspective to focus on the post-processing step.ResultsUsing both the assembled contigs and original long reads as input, BIGMAC first breaks the contigs at potentially mis-assembled locations and subsequently scaffolds contigs. Our experiments on metagenomes assembled from long reads show that BIGMAC can improve assembly quality by reducing the number of mis-assemblies while maintaining or increasing N50 and N75. Moreover, BIGMAC shows the largest N75 to number of mis-assemblies ratio on all tested datasets when compared to other post-processing tools.ConclusionsBIGMAC demonstrates the effectiveness of the post-processing approach in improving the quality of metagenomic assemblies

The retrieval of fingerprint friction ridge detail from elephant ivory using reduced-scale magnetic and non-magnetic powdering materials

An evaluation of reduced-size particle powdering methods for the recovery of usable fingermark ridge detail from elephant ivory is presented herein for the first time as a practical and cost-effective tool in forensic analysis. Of two reduced-size powder material types tested, powders with particle sizes≤40μm offered better chances of recovering ridge detail from unpolished ivory in comparison to a conventional powder material. The quality of developed ridge detail of these powders was also assessed for comparison and automated search suitability. Powder materials and the enhanced ridge detail on ivory were analysed by scanning electron microscopy and energy dispersive X-ray spectroscopy and interactions between their constituents and the ivory discussed. The effect of ageing on the quality of ridge detail recovered showed that the best quality was obtained within 1week. However, some ridge detail could still be developed up to 28days after deposition. Cyanoacrylate and fluorescently-labelled cyanoacrylate fuming of ridge detail on ivory was explored and was less effective than reduced-scale powdering in general. This research contributes to the understanding and potential application of smaller scale powdering materials for the development of ridge detail on hard, semi-porous biological material typically seized in wildlife-related crimes

Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes

Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization

Value-based analysis of routine pathologic septal and inferior turbinate specimens.

This article was presented at the 2012 AAO-HNSF Annual Meeting & OTO EXPO; September 9-12, 2012; Washington, DC. Objective To determine the frequency and clinical relevance of unanticipated histopathologic results in routine sinonasal surgery and evaluate the necessity for histologic processing of nasal septal cartilage, bone, and inferior turbinate specimens. Study Design Case series with chart review. Setting Tertiary care academic medical center. Subjects and Methods A retrospective review of surgical pathology reports on adult patients undergoing sinonasal surgery during a 5-year period from 2005 to 2010 was performed. All cases with the preoperative diagnosis of sinonasal neoplasia, autoimmune disease, or directed septal biopsies were excluded from review. Results A total of 1194 pathology reports were reviewed from 1172 individual patients. This included histopathologic evaluation of 1194 septal cartilage and bone specimens and 714 inferior turbinate specimens. None of the patients had unanticipated histopathologic findings that were clinically significant. Conclusion Many surgeons obtain histopathologic diagnoses on all tissue removed from a patient. Based on our institutional case series, histopathology of the septum and inferior turbinates in routine sinonasal cases may not be necessary. A value-based approach to processing grossly unremarkable septal and turbinate tissue by waiving histologic processing and subsequent microscopic evaluation could provide significant cost savings